diff --git a/.changeset/repeat-install-verify-deps-unification.md b/.changeset/repeat-install-verify-deps-unification.md
index 0b3fdcc2cf..c9eadc891b 100644
--- a/.changeset/repeat-install-verify-deps-unification.md
+++ b/.changeset/repeat-install-verify-deps-unification.md
@@ -3,9 +3,10 @@
 "@pnpm/exec.commands": patch
 "@pnpm/installing.commands": patch
 "@pnpm/installing.deps-restorer": patch
+"@pnpm/workspace.projects-graph": patch
 "@pnpm/workspace.state": patch
 "pnpm": patch
 "pacquet": patch
 ---
 
-`pnpm run`, `pnpm exec`, and `pnpm restart` now pass the install flags they were given, such as `--lockfile-dir`, `--modules-dir`, `--store-dir`, `--offline`, and `--ignore-scripts`, to the `pnpm install` that `verifyDepsBeforeRun: install` starts. The check that runs before a script now holds the workspace projects the script's project depends on. It agrees with the repeat-install check on which projects a filtered install left uninstalled, including with per-project lockfiles. A filtered install no longer forgets the ignored build scripts of the projects it did not select.
+`pnpm run`, `pnpm exec`, and `pnpm restart` now pass the install flags they were given, such as `--lockfile-dir`, `--modules-dir`, `--store-dir`, `--offline`, and `--ignore-scripts`, to the `pnpm install` that `verifyDepsBeforeRun: install` starts. The check that runs before a script now holds the workspace projects the script's project depends on. It agrees with the repeat-install check on which projects a filtered install left uninstalled, including with per-project lockfiles. Workspace dependencies declared with `link:` are now included in the workspace project graph, so `--filter=<project>...` selects them and, with `sharedWorkspaceLockfile: false` and `injectWorkspacePackages: true`, the check before a script still requires them to be installed. A filtered install no longer forgets the ignored build scripts of the projects it did not select.
diff --git a/pnpm/crates/cli/src/cli_args/recursive.rs b/pnpm/crates/cli/src/cli_args/recursive.rs
index 702539520b..537f3e27df 100644
--- a/pnpm/crates/cli/src/cli_args/recursive.rs
+++ b/pnpm/crates/cli/src/cli_args/recursive.rs
@@ -7,9 +7,7 @@
 //! command-specific error codes) live in `run/recursive.rs` and
 //! `exec/recursive.rs`.
 
-pub use dependencies::{
-    filtered_projects_dependencies, projects_with_workspace_dependencies, sequence_graph,
-};
+pub use dependencies::{filtered_projects_dependencies, projects_to_verify, sequence_graph};
 pub use execution_args::RecursiveExecutionArgs;
 pub use importer_selection::{selected_workspace_importer_ids, selectors_narrow_the_run};
 pub use summary::{ExecutionStatus, Status, count_failures, write_recursive_summary};
@@ -20,10 +18,7 @@ mod execution_args;
 mod importer_selection;
 mod unmatched;
 
-use crate::cli_args::{
-    catalogs::{configured_catalogs, workspace_catalogs},
-    verify_deps::with_dependencies,
-};
+use crate::cli_args::catalogs::{configured_catalogs, workspace_catalogs};
 use derive_more::{Display, Error};
 use indexmap::IndexMap;
 use miette::{Context, Diagnostic, IntoDiagnostic};
@@ -150,84 +145,6 @@ impl<'a> RecursiveSelection<'a> {
     }
 }
 
-/// The projects a gated recursive command holds to the modules-directory
-/// requirement: `project_dirs` themselves, plus every workspace dependency
-/// they reach that the installs the gate spawns cover.
-///
-/// A workspace dependency that is not installed leaves the selection out of
-/// date too. With one shared lockfile, the install the gate spawns selects the
-/// dependencies of the selected projects, and a negated selector reaches it
-/// unchanged, so a dependency it excludes is not required; `project_dirs`
-/// themselves always are. With a lockfile per project the gate checks and
-/// installs each project on its own, and a workspace dependency the project
-/// injects is part of that project's own install. `prefix` is where the
-/// command's path selectors resolve.
-pub fn projects_to_verify<'dirs>(
-    project_dirs: impl IntoIterator<Item = &'dirs Path>,
-    selection: &RecursiveSelection<'_>,
-    config: &Config,
-    prefix: &Path,
-) -> miette::Result<Vec<PathBuf>> {
-    if !config.verify_deps_before_run.is_enabled() {
-        return Ok(Vec::new());
-    }
-    let project_dirs: Vec<&Path> = project_dirs.into_iter().collect();
-    // An injected workspace dependency is a copy inside the project that
-    // depends on it, which that project's own install covers.
-    if !config.shares_one_lockfile() && config.inject_workspace_packages {
-        return Ok(project_dirs
-            .into_iter()
-            .map(Path::to_path_buf)
-            .collect());
-    }
-    let mut projects = projects_with_workspace_dependencies(
-        project_dirs.iter().copied(),
-        selection.full_graph(),
-        selection.prod_all.as_ref(),
-        &selection.prod_only_selected,
-    );
-    if config.shares_one_lockfile() && has_negated_selector(config) {
-        let mut kept = install_selected_projects(selection, config, prefix)?;
-        kept.extend(project_dirs.iter().map(|dir| dir.to_path_buf()));
-        projects.retain(|project_dir| kept.contains(project_dir));
-    }
-    Ok(projects)
-}
-
-fn has_negated_selector(config: &Config) -> bool {
-    config.filter
-        .iter()
-        .chain(&config.filter_prod)
-        .any(|selector| selector.starts_with('!'))
-}
-
-/// The projects the install the gate spawns selects, evaluated against the
-/// graphs the command's own selection was drawn from.
-fn install_selected_projects(
-    selection: &RecursiveSelection<'_>,
-    config: &Config,
-    prefix: &Path,
-) -> miette::Result<HashSet<PathBuf>> {
-    let walk_opts = recursive_filter_options(config, prefix);
-    let filter = with_dependencies_selectors(&config.filter);
-    let mut installed: HashSet<PathBuf> =
-        filter_against(selection.full_graph(), &filter, None, false, prefix, &walk_opts)?
-            .into_iter()
-            .collect();
-    if let Some(prod_all) = &selection.prod_all {
-        let filter_prod = with_dependencies_selectors(&config.filter_prod);
-        installed.extend(filter_against(prod_all, &filter_prod, None, true, prefix, &walk_opts)?);
-    }
-    Ok(installed)
-}
-
-fn with_dependencies_selectors(selectors: &[String]) -> Vec<String> {
-    selectors
-        .iter()
-        .map(|selector| with_dependencies(selector))
-        .collect()
-}
-
 /// Build the `--filter`-selected workspace projects the recursive command
 /// runs over, together with the graphs [`filtered_projects_dependencies`] resolves
 /// order through. `prefix` is where path selectors resolve; `auto_exclude_root`
diff --git a/pnpm/crates/cli/src/cli_args/recursive/dependencies.rs b/pnpm/crates/cli/src/cli_args/recursive/dependencies.rs
index 88fb1df15a..28571032e8 100644
--- a/pnpm/crates/cli/src/cli_args/recursive/dependencies.rs
+++ b/pnpm/crates/cli/src/cli_args/recursive/dependencies.rs
@@ -2,9 +2,20 @@
 //! dependency edges among the `--filter`-selected projects, their topological
 //! order, and the workspace dependencies a selection reaches.
 
+use super::{RecursiveSelection, filter_against, recursive_filter_options};
+use crate::cli_args::{
+    catalogs::{configured_catalogs, workspace_catalogs},
+    verify_deps::with_dependencies,
+};
 use indexmap::IndexMap;
+use pnpm_catalogs_resolver::{
+    CatalogAnchor, CatalogResolutionResult, WantedDependency, resolve_from_catalog,
+};
+use pnpm_config::Config;
+use pnpm_fs::lexical_normalize;
 use pnpm_package_manager::{GraphSequencerResult, graph_sequencer};
-use pnpm_workspace_projects_graph::ProjectGraph;
+use pnpm_package_manifest::{DependencyGroup, PackageManifest};
+use pnpm_workspace_projects_graph::{ProjectGraph, WorkspaceCatalogs};
 use rayon::prelude::*;
 use std::{
     collections::{HashMap, HashSet},
@@ -123,8 +134,158 @@ fn sorted_dependencies<Pkg>(
     dependencies
 }
 
+/// The projects a gated recursive command holds to the modules-directory
+/// requirement: `project_dirs` themselves, plus every workspace dependency
+/// they reach that the installs the gate spawns cover.
+///
+/// A workspace dependency that is not installed leaves the selection out of
+/// date too. With one shared lockfile, the install the gate spawns selects the
+/// dependencies of the selected projects, and a negated selector reaches it
+/// unchanged, so a dependency it excludes is not required; `project_dirs`
+/// themselves always are. With a lockfile per project the gate checks and
+/// installs each project on its own, and a workspace dependency the project
+/// injects is part of that project's own install. `prefix` is where the
+/// command's path selectors resolve.
+pub fn projects_to_verify<'dirs>(
+    project_dirs: impl IntoIterator<Item = &'dirs Path>,
+    selection: &RecursiveSelection<'_>,
+    config: &Config,
+    prefix: &Path,
+) -> miette::Result<Vec<PathBuf>> {
+    if !config.verify_deps_before_run.is_enabled() {
+        return Ok(Vec::new());
+    }
+    let project_dirs: Vec<&Path> = project_dirs.into_iter().collect();
+    // An injected workspace dependency is a copy inside the project that
+    // depends on it, which that project's own install covers; explicit `link:`
+    // dependencies remain symlinks and still need their target project installed.
+    let only_linked = !config.shares_one_lockfile() && config.inject_workspace_packages;
+    let catalogs = if only_linked { Some(configured_catalogs(config)?) } else { None };
+    let ws_catalogs = catalogs.as_ref().and_then(|catalogs| workspace_catalogs(config, catalogs));
+    let mut projects = projects_with_workspace_dependencies_filtered(
+        project_dirs.iter().copied(),
+        selection.full_graph(),
+        selection.prod_all.as_ref(),
+        &selection.prod_only_selected,
+        |parent_dir, pkg, deps| {
+            retained_dependency_dirs(
+                parent_dir,
+                &pkg.project.manifest,
+                deps,
+                only_linked,
+                ws_catalogs,
+            )
+        },
+    );
+    if config.shares_one_lockfile() && has_negated_selector(config) {
+        let mut kept = install_selected_projects(selection, config, prefix)?;
+        kept.extend(project_dirs.iter().map(|dir| dir.to_path_buf()));
+        projects.retain(|project_dir| kept.contains(project_dir));
+    }
+    Ok(projects)
+}
+
+fn retained_dependency_dirs<'graph>(
+    parent_dir: &Path,
+    manifest: &PackageManifest,
+    deps: &'graph [PathBuf],
+    only_linked: bool,
+    catalogs: Option<WorkspaceCatalogs<'_>>,
+) -> Vec<&'graph Path> {
+    if !only_linked || deps.is_empty() {
+        return deps
+            .iter()
+            .map(PathBuf::as_path)
+            .collect();
+    }
+    let linked = linked_dependency_dirs(parent_dir, manifest, catalogs);
+    deps.iter()
+        .map(PathBuf::as_path)
+        .filter(|dep_dir| linked.contains(&lexical_normalize(dep_dir)))
+        .collect()
+}
+
+fn linked_dependency_dirs(
+    parent_dir: &Path,
+    manifest: &PackageManifest,
+    catalogs: Option<WorkspaceCatalogs<'_>>,
+) -> rustc_hash::FxHashSet<PathBuf> {
+    manifest
+        .dependencies([
+            DependencyGroup::Prod,
+            DependencyGroup::Dev,
+            DependencyGroup::Optional,
+            DependencyGroup::Peer,
+        ])
+        .filter_map(|(dep_name, raw_spec)| {
+            let resolved = resolve_catalog_spec(parent_dir, dep_name, raw_spec, catalogs);
+            let spec = resolved.as_deref().unwrap_or(raw_spec);
+            let rel = spec.strip_prefix("link:")?;
+            Some(lexical_normalize(&parent_dir.join(rel.replace('\\', "/"))))
+        })
+        .collect()
+}
+
+fn resolve_catalog_spec(
+    consumer_dir: &Path,
+    dep_name: &str,
+    raw_spec: &str,
+    catalogs: Option<WorkspaceCatalogs<'_>>,
+) -> Option<String> {
+    let catalogs = catalogs?;
+    if !raw_spec.starts_with("catalog:") {
+        return None;
+    }
+    let wanted =
+        WantedDependency { alias: dep_name.to_string(), bare_specifier: raw_spec.to_string() };
+    let anchor = CatalogAnchor::Reanchor {
+        workspace_dir: catalogs.workspace_dir,
+        consumer_dir: Some(consumer_dir),
+    };
+    match resolve_from_catalog(catalogs.catalogs, &wanted, anchor) {
+        CatalogResolutionResult::Found(found) => Some(found.resolution.specifier),
+        CatalogResolutionResult::Misconfiguration(_) | CatalogResolutionResult::Unused => None,
+    }
+}
+
+fn has_negated_selector(config: &Config) -> bool {
+    config.filter
+        .iter()
+        .chain(&config.filter_prod)
+        .any(|selector| selector.starts_with('!'))
+}
+
+/// The projects the install the gate spawns selects, evaluated against the
+/// graphs the command's own selection was drawn from.
+fn install_selected_projects(
+    selection: &RecursiveSelection<'_>,
+    config: &Config,
+    prefix: &Path,
+) -> miette::Result<HashSet<PathBuf>> {
+    let walk_opts = recursive_filter_options(config, prefix);
+    let filter = with_dependencies_selectors(&config.filter);
+    let mut installed: HashSet<PathBuf> =
+        filter_against(selection.full_graph(), &filter, None, false, prefix, &walk_opts)?
+            .into_iter()
+            .collect();
+    if let Some(prod_all) = &selection.prod_all {
+        let filter_prod = with_dependencies_selectors(&config.filter_prod);
+        installed.extend(filter_against(prod_all, &filter_prod, None, true, prefix, &walk_opts)?);
+    }
+    Ok(installed)
+}
+
+fn with_dependencies_selectors(selectors: &[String]) -> Vec<String> {
+    selectors
+        .iter()
+        .map(|selector| with_dependencies(selector))
+        .collect()
+}
+
 /// `project_dirs` together with every workspace project they depend on,
-/// directly or transitively.
+/// directly or transitively, along the dependency edges that `filter_edges`
+/// retains for each parent node `(parent_dir, &parent_node.package,
+/// &parent_node.dependencies)`.
 ///
 /// The install a gated command spawns selects the dependencies of the projects
 /// the command selected, so a project whose workspace dependency has no modules
@@ -135,14 +296,18 @@ fn sorted_dependencies<Pkg>(
 ///
 /// Each graph keeps one visited set across all roots, so a dependency shared
 /// by several selected projects is walked once.
-pub fn projects_with_workspace_dependencies<'graph, 'dirs, Pkg>(
+pub(super) fn projects_with_workspace_dependencies_filtered<'graph, 'dirs, Pkg, Filter>(
     project_dirs: impl IntoIterator<Item = &'dirs Path>,
     all: &'graph ProjectGraph<Pkg>,
     prod_all: Option<&'graph ProjectGraph<Pkg>>,
     prod_only_selected: &HashSet<PathBuf>,
-) -> Vec<PathBuf> {
-    let mut all_walk = DependencyWalk::new(all);
-    let mut prod_walk = prod_all.map(DependencyWalk::new);
+    filter_edges: Filter,
+) -> Vec<PathBuf>
+where
+    Filter: Fn(&Path, &Pkg, &'graph [PathBuf]) -> Vec<&'graph Path>,
+{
+    let mut all_walk = DependencyWalk::new(all, &filter_edges);
+    let mut prod_walk = prod_all.map(|graph| DependencyWalk::new(graph, &filter_edges));
     let mut outside_graph: Vec<&Path> = Vec::new();
     for project_dir in project_dirs {
         let walk = match &mut prod_walk {
@@ -164,16 +329,25 @@ pub fn projects_with_workspace_dependencies<'graph, 'dirs, Pkg>(
 }
 
 /// A walk along the dependency edges of one graph, from any number of roots.
-struct DependencyWalk<'graph, Pkg> {
+struct DependencyWalk<'graph, 'filter, Pkg, Filter> {
     graph: &'graph ProjectGraph<Pkg>,
+    filter_edges: &'filter Filter,
     seen: rustc_hash::FxHashSet<&'graph Path>,
     /// The projects reached, in the order they were first reached.
     visited: Vec<&'graph Path>,
 }
 
-impl<'graph, Pkg> DependencyWalk<'graph, Pkg> {
-    fn new(graph: &'graph ProjectGraph<Pkg>) -> Self {
-        DependencyWalk { graph, seen: rustc_hash::FxHashSet::default(), visited: Vec::new() }
+impl<'graph, 'filter, Pkg, Filter> DependencyWalk<'graph, 'filter, Pkg, Filter>
+where
+    Filter: Fn(&Path, &Pkg, &'graph [PathBuf]) -> Vec<&'graph Path>,
+{
+    fn new(graph: &'graph ProjectGraph<Pkg>, filter_edges: &'filter Filter) -> Self {
+        DependencyWalk {
+            graph,
+            filter_edges,
+            seen: rustc_hash::FxHashSet::default(),
+            visited: Vec::new(),
+        }
     }
 
     /// Visit `root` and every project reachable from it that no earlier root
@@ -187,17 +361,15 @@ impl<'graph, Pkg> DependencyWalk<'graph, Pkg> {
             return true;
         }
         self.visited.push(root.as_path());
-        let mut stack: Vec<&'graph Path> = node.dependencies
-            .iter()
-            .map(PathBuf::as_path)
-            .collect();
+        let mut stack: Vec<&'graph Path> =
+            (self.filter_edges)(root, &node.package, &node.dependencies);
         while let Some(project_dir) = stack.pop() {
             if !self.seen.insert(project_dir) {
                 continue;
             }
             self.visited.push(project_dir);
             if let Some(node) = self.graph.get(project_dir) {
-                stack.extend(node.dependencies.iter().map(PathBuf::as_path));
+                stack.extend((self.filter_edges)(project_dir, &node.package, &node.dependencies));
             }
         }
         true
diff --git a/pnpm/crates/cli/src/cli_args/recursive/tests.rs b/pnpm/crates/cli/src/cli_args/recursive/tests.rs
index d4a688f331..ca09d9c4b5 100644
--- a/pnpm/crates/cli/src/cli_args/recursive/tests.rs
+++ b/pnpm/crates/cli/src/cli_args/recursive/tests.rs
@@ -6,15 +6,41 @@
 //! selection resolves through the prod-pruned graph so the dev edges it
 //! dropped are not pulled back in.
 
-use super::{filtered_projects_dependencies, projects_with_workspace_dependencies, sequence_graph};
+use super::{
+    RecursiveSelection, dependencies::projects_with_workspace_dependencies_filtered,
+    filtered_projects_dependencies, projects_to_verify, sequence_graph,
+};
+use pnpm_config::{Config, VerifyDepsBeforeRun};
 use pnpm_package_manager::graph_sequencer;
+use pnpm_package_manifest::PackageManifest;
+use pnpm_workspace::{GraphPkg, Project};
 use pnpm_workspace_projects_graph::{ProjectGraph, ProjectGraphNode};
 use pretty_assertions::assert_eq;
 use std::{
     collections::{HashMap, HashSet},
+    fs,
     path::{Path, PathBuf},
 };
 
+fn projects_with_workspace_dependencies<'graph, 'dirs, Pkg>(
+    project_dirs: impl IntoIterator<Item = &'dirs Path>,
+    all: &'graph ProjectGraph<Pkg>,
+    prod_all: Option<&'graph ProjectGraph<Pkg>>,
+    prod_only_selected: &HashSet<PathBuf>,
+) -> Vec<PathBuf> {
+    projects_with_workspace_dependencies_filtered(
+        project_dirs,
+        all,
+        prod_all,
+        prod_only_selected,
+        |_, _, deps| {
+            deps.iter()
+                .map(PathBuf::as_path)
+                .collect()
+        },
+    )
+}
+
 fn make_graph(adjacency: &[(&str, &[&str])]) -> ProjectGraph<()> {
     adjacency
         .iter()
@@ -253,3 +279,80 @@ fn projects_with_workspace_dependencies_lists_a_shared_dependency_once() {
         dirs(&["a", "c", "b"]),
     );
 }
+
+#[test]
+fn projects_to_verify_under_dedicated_lockfiles_with_injection_follows_only_link_edges() {
+    let tmp = tempfile::tempdir().unwrap();
+    fs::write(
+        tmp.path().join("pnpm-workspace.yaml"),
+        "packages:\n  - '*'\ncatalog:\n  d: link:./d\n",
+    )
+    .unwrap();
+    let write_project = |name: &str, json: &str| {
+        let dir = tmp.path().join(name);
+        fs::create_dir_all(&dir).unwrap();
+        let manifest_path = dir.join("package.json");
+        fs::write(&manifest_path, json).unwrap();
+        Project {
+            root_dir: dir,
+            manifest: PackageManifest::from_path(manifest_path).unwrap(),
+            dependency_manifest: None,
+        }
+    };
+    let pkg_a = write_project(
+        "a",
+        r#"{"name":"a","version":"1.0.0","dependencies":{"b":"workspace:*","c":"link:../c","d":"catalog:"}}"#,
+    );
+    let pkg_b = write_project("b", r#"{"name":"b","version":"1.0.0"}"#);
+    let pkg_c = write_project("c", r#"{"name":"c","version":"1.0.0"}"#);
+    let pkg_d = write_project("d", r#"{"name":"d","version":"1.0.0"}"#);
+    let all: ProjectGraph<GraphPkg<'_>> = [
+        (
+            pkg_a.root_dir.clone(),
+            ProjectGraphNode {
+                package: GraphPkg { project: &pkg_a },
+                dependencies: vec![
+                    pkg_b.root_dir.clone(),
+                    pkg_c.root_dir.clone(),
+                    pkg_d.root_dir.clone(),
+                ],
+            },
+        ),
+        (
+            pkg_b.root_dir.clone(),
+            ProjectGraphNode { package: GraphPkg { project: &pkg_b }, dependencies: Vec::new() },
+        ),
+        (
+            pkg_c.root_dir.clone(),
+            ProjectGraphNode { package: GraphPkg { project: &pkg_c }, dependencies: Vec::new() },
+        ),
+        (
+            pkg_d.root_dir.clone(),
+            ProjectGraphNode { package: GraphPkg { project: &pkg_d }, dependencies: Vec::new() },
+        ),
+    ]
+    .into_iter()
+    .collect();
+    let selected =
+        std::iter::once((pkg_a.root_dir.clone(), all[&pkg_a.root_dir].clone())).collect();
+    let selection = RecursiveSelection {
+        selected,
+        all: Some(all),
+        prod_all: None,
+        prod_only_selected: HashSet::new(),
+    };
+    let config = Config {
+        verify_deps_before_run: VerifyDepsBeforeRun::Error,
+        shared_workspace_lockfile: false,
+        inject_workspace_packages: true,
+        workspace_dir: Some(tmp.path().to_path_buf()),
+        ..Config::default()
+    };
+
+    let mut verified =
+        projects_to_verify([pkg_a.root_dir.as_path()], &selection, &config, tmp.path()).unwrap();
+    verified.sort();
+    let mut expected = vec![pkg_a.root_dir, pkg_c.root_dir, pkg_d.root_dir];
+    expected.sort();
+    assert_eq!(verified, expected);
+}
diff --git a/pnpm/crates/cli/tests/suite/verify_deps_before_run.rs b/pnpm/crates/cli/tests/suite/verify_deps_before_run.rs
index 506811d31a..0cbed0aa98 100644
--- a/pnpm/crates/cli/tests/suite/verify_deps_before_run.rs
+++ b/pnpm/crates/cli/tests/suite/verify_deps_before_run.rs
@@ -1683,6 +1683,141 @@ fn filtered_exec_installs_a_workspace_dependency_a_filtered_install_left_alone()
     drop((root, mock_instance));
 }
 
+/// Under dedicated lockfiles with `injectWorkspacePackages`, an injected
+/// `workspace:*` dependency is a copy inside the dependent project that its
+/// own install covers, whereas an explicit `link:` dependency remains a
+/// symlink whose target project must still be installed
+/// ([pnpm/tasks#179](https://github.com/pnpm/tasks/issues/179)).
+#[test]
+fn filtered_exec_holds_a_link_dependency_under_dedicated_lockfiles_with_injection() {
+    let CommandTempCwd { root, workspace, npmrc_info, .. } =
+        CommandTempCwd::init().add_mocked_registry();
+    let AddMockedRegistry { mock_instance, .. } = npmrc_info;
+    fs::write(
+        workspace.join("package.json"),
+        json!({ "name": "workspace-root", "version": "0.0.0" }).to_string(),
+    )
+    .expect("write root package.json");
+    fs::write(
+        workspace.join("pnpm-workspace.yaml"),
+        "sharedWorkspaceLockfile: false\ninjectWorkspacePackages: true\npackages:\n  - packages/*\n",
+    )
+    .expect("write pnpm-workspace.yaml");
+    let projects = [
+        ("foo", json!({ "dependencies": { "bar": "workspace:*" } })),
+        ("bar", json!({ "dependencies": { "@pnpm.e2e/foo": "100.0.0" } })),
+        ("baz", json!({ "dependencies": { "@pnpm.e2e/foo": "100.0.0" } })),
+    ];
+    for (name, groups) in projects {
+        let project = workspace.join("packages").join(name);
+        fs::create_dir_all(&project).expect("create workspace project");
+        write_named_manifest_with_dependency_groups(
+            &project,
+            name,
+            &project.join("marker.txt"),
+            groups,
+        );
+    }
+
+    pacquet_in(&workspace)
+        .with_args(["--filter", "foo", "install"])
+        .assert()
+        .success();
+    assert!(!workspace.join("packages/bar/node_modules").exists());
+
+    // An injected `workspace:*` dependency is covered by `foo`'s own install,
+    // so an uninstalled `bar` does not block a filtered exec on `foo`.
+    let output = pacquet_in(&workspace)
+        .with_args([
+            "--config.verify-deps-before-run=error",
+            "--filter",
+            "foo",
+            "exec",
+            "node",
+            "-e",
+            r#"process.stdout.write("injected-ok")"#,
+        ])
+        .output()
+        .expect("spawn pacquet exec");
+    let stderr = String::from_utf8_lossy(&output.stderr);
+    assert!(
+        output.status.success(),
+        "an uninstalled injected workspace dependency must not block the filtered exec:\n{stderr}",
+    );
+    assert_eq!(String::from_utf8_lossy(&output.stdout), "injected-ok");
+
+    // Adding a `link:` dependency to `baz` and installing `foo` alone leaves
+    // `baz` without a modules directory; `link:` remains a symlink even with
+    // injection on, so the gate holds `baz` to the modules-directory check.
+    write_named_manifest_with_dependency_groups(
+        &workspace.join("packages/foo"),
+        "foo",
+        &workspace.join("packages/foo/marker.txt"),
+        json!({ "dependencies": { "bar": "workspace:*", "baz": "link:../baz" } }),
+    );
+    pacquet_in(&workspace)
+        .with_args(["--filter", "foo", "install"])
+        .assert()
+        .success();
+    assert!(!workspace.join("packages/baz/node_modules").exists());
+
+    let output = pacquet_in(&workspace)
+        .with_args([
+            "--config.verify-deps-before-run=error",
+            "--filter",
+            "foo",
+            "exec",
+            "node",
+            "-e",
+            "0",
+        ])
+        .output()
+        .expect("spawn pacquet exec");
+    let stderr = String::from_utf8_lossy(&output.stderr);
+    assert!(
+        !output.status.success() && stderr.contains("ERR_PNPM_VERIFY_DEPS_BEFORE_RUN"),
+        "a never-installed link: dependency must fail the verify-deps check:\n{stderr}",
+    );
+
+    let output = pacquet_in(&workspace)
+        .with_args([
+            "--config.verify-deps-before-run=install",
+            "--filter",
+            "foo",
+            "exec",
+            "node",
+            "-e",
+            r#"process.stdout.write("linked-ok")"#,
+        ])
+        .output()
+        .expect("spawn pacquet exec");
+    let stderr = String::from_utf8_lossy(&output.stderr);
+    assert!(
+        output.status.success(),
+        "the filtered exec must install the link: dependency:\n{stderr}",
+    );
+    assert_eq!(String::from_utf8_lossy(&output.stdout), "linked-ok");
+    assert!(
+        workspace.join("packages/baz/node_modules/@pnpm.e2e/foo").exists(),
+        "the gate must install the link: dependency:\n{stderr}",
+    );
+
+    pacquet_in(&workspace)
+        .with_args([
+            "--config.verify-deps-before-run=error",
+            "--filter",
+            "foo",
+            "exec",
+            "node",
+            "-e",
+            "0",
+        ])
+        .assert()
+        .success();
+
+    drop((root, mock_instance));
+}
+
 /// A negated selector reaches the install the gate spawns unchanged, so that
 /// install never materializes the project it excludes. The status check must
 /// not hold that project to the modules-directory requirement through the
diff --git a/pnpm/crates/package-manager/src/install/workspace_state/discovery.rs b/pnpm/crates/package-manager/src/install/workspace_state/discovery.rs
index d0416a4eb1..618886ad4b 100644
--- a/pnpm/crates/package-manager/src/install/workspace_state/discovery.rs
+++ b/pnpm/crates/package-manager/src/install/workspace_state/discovery.rs
@@ -60,7 +60,7 @@ pub fn check_deps_status_before_run_at(
         return cannot_check_deps();
     };
     let workspace_manifest = workspace_manifest.flatten();
-    let config = gate_config(config, manifest_dir, &manifest);
+    let config = gate_config(config, workspace_dir_opt.as_deref(), manifest_dir, &manifest);
     // A pinned `lockfileDir` is where the install left the state and the
     // lockfile; otherwise it follows the manifest read above, just as it
     // does during install.
@@ -142,20 +142,26 @@ pub fn deps_install_root(dir: &Path, config: &Config) -> std::path::PathBuf {
 }
 fn gate_config<'a>(
     config: &'a Config,
+    workspace_dir: Option<&Path>,
     manifest_dir: &Path,
     manifest: &PackageManifest,
 ) -> Cow<'a, Config> {
-    if config.shares_one_lockfile() {
-        Cow::Borrowed(config)
-    } else {
-        let mut project_config = config.clone();
+    let needs_workspace_dir = config.workspace_dir.is_none() && workspace_dir.is_some();
+    if config.shares_one_lockfile() && !needs_workspace_dir {
+        return Cow::Borrowed(config);
+    }
+    let mut project_config = config.clone();
+    if needs_workspace_dir {
+        project_config.workspace_dir = workspace_dir.map(Path::to_path_buf);
+    }
+    if !config.shares_one_lockfile() {
         let project_name = manifest
             .value()
             .get("name")
             .and_then(serde_json::Value::as_str);
         project_config.anchor_dedicated_project(manifest_dir, project_name);
-        Cow::Owned(project_config)
     }
+    Cow::Owned(project_config)
 }
 pub(super) fn cannot_check_deps() -> Option<crate::RunDepsStatus> {
     Some(crate::RunDepsStatus::Outdated {
diff --git a/pnpm/crates/package-manager/src/optimistic_repeat_install/modules_dirs.rs b/pnpm/crates/package-manager/src/optimistic_repeat_install/modules_dirs.rs
index d7d5f9d343..d2cc24eec7 100644
--- a/pnpm/crates/package-manager/src/optimistic_repeat_install/modules_dirs.rs
+++ b/pnpm/crates/package-manager/src/optimistic_repeat_install/modules_dirs.rs
@@ -1,23 +1,23 @@
+mod workspace_deps;
+
 use super::{
-    CatalogAnchor, CatalogResolutionResult, Catalogs, OptimisticRepeatInstallCheck,
-    WantedDependency, manifest_has_required_peers, manifest_has_runtime_deps,
-    manifest_string_field, resolve_from_catalog,
+    OptimisticRepeatInstallCheck, manifest_has_required_peers, manifest_has_runtime_deps,
+    manifest_string_field,
 };
 use pnpm_config::{Config, NodeLinker};
 use pnpm_fs::lexical_normalize;
 use pnpm_lockfile::{MaybeLazyLockfile, PkgName, ProjectSnapshot, ResolvedDependencySpec};
 use pnpm_modules_yaml::IncludedDependencies;
 use pnpm_package_manifest::{DependencyGroup, PackageManifest};
-use pnpm_semver_include_prerelease::IncludePrereleaseRange;
 use pnpm_workspace::importer_id_from_root_dir;
 use pnpm_workspace_state::WorkspaceState;
 use rayon::prelude::*;
 use std::{
-    borrow::Cow,
-    collections::{HashMap, HashSet},
+    collections::HashSet,
     fs,
     path::{Path, PathBuf},
 };
+use workspace_deps::reached_workspace_project_dirs;
 
 /// The id (`name` field, falling back to the root dir) of the first
 /// project that declares dependencies but has no modules directory, or
@@ -49,151 +49,6 @@ pub(super) fn first_selected_project_missing_modules_dir(
         selected.contains(&lexical_normalize(root_dir))
     })
 }
-
-struct WorkspaceProjectIndex<'a> {
-    by_dir: HashMap<PathBuf, &'a PackageManifest>,
-    by_name: HashMap<String, Vec<(PathBuf, Option<String>)>>,
-    link_workspace_packages: bool,
-    catalogs: &'a Catalogs,
-}
-
-impl<'a> WorkspaceProjectIndex<'a> {
-    fn from_check(check: &OptimisticRepeatInstallCheck<'a>) -> Self {
-        let mut by_dir = HashMap::new();
-        let mut by_name: HashMap<String, Vec<(PathBuf, Option<String>)>> = HashMap::new();
-        for (dir, manifest) in check.project_manifests {
-            let norm = lexical_normalize(dir);
-            by_dir.insert(norm.clone(), *manifest);
-            if let Some(name) = manifest_string_field(manifest, "name") {
-                let version = manifest_string_field(manifest, "version");
-                by_name
-                    .entry(name)
-                    .or_default()
-                    .push((norm, version));
-            }
-        }
-        Self {
-            by_dir,
-            by_name,
-            link_workspace_packages: check.config.link_workspace_packages.enabled_at_depth(0),
-            catalogs: check.catalogs,
-        }
-    }
-
-    fn dereference_catalog<'b>(&self, alias: &str, spec: &'b str) -> Option<Cow<'b, str>> {
-        if !spec.starts_with("catalog:") {
-            return Some(Cow::Borrowed(spec));
-        }
-        let CatalogResolutionResult::Found(found) = resolve_from_catalog(
-            self.catalogs,
-            &WantedDependency { alias: alias.to_string(), bare_specifier: spec.to_string() },
-            CatalogAnchor::AsWritten,
-        ) else {
-            return None;
-        };
-        Some(Cow::Owned(found.resolution.specifier))
-    }
-
-    fn dep_targets(&self, dir: &Path, alias: &str, spec: &str) -> Vec<PathBuf> {
-        let Some(spec) = self.dereference_catalog(alias, spec) else {
-            return Vec::new();
-        };
-        let spec = spec.as_ref();
-        if let Some(rel) = spec
-            .strip_prefix("link:")
-            .or_else(|| spec.strip_prefix("file:"))
-        {
-            return self.resolve_dir_target(dir, rel);
-        }
-        let is_workspace = spec.starts_with("workspace:");
-        if !is_workspace && !self.link_workspace_packages {
-            return Vec::new();
-        }
-        if let Some(ws_spec) = spec.strip_prefix("workspace:")
-            && is_relative_workspace_path(ws_spec)
-        {
-            return self.resolve_dir_target(dir, ws_spec);
-        }
-        let (target_name, range) = crate::install::spec_target_and_range(spec);
-        let name = target_name.unwrap_or(alias);
-        self.by_name
-            .get(name)
-            .into_iter()
-            .flatten()
-            .filter(|(_, version)| {
-                workspace_version_matches_range(version.as_deref(), range, is_workspace)
-            })
-            .map(|(dir, _)| dir.clone())
-            .collect()
-    }
-
-    fn resolve_dir_target(&self, dir: &Path, rel: &str) -> Vec<PathBuf> {
-        let normalized_rel = rel.replace('\\', "/");
-        let target = lexical_normalize(&dir.join(normalized_rel));
-        self.by_dir
-            .contains_key(&target)
-            .then_some(target)
-            .into_iter()
-            .collect()
-    }
-}
-
-fn is_relative_workspace_path(ws_spec: &str) -> bool {
-    matches!(ws_spec, "." | "..")
-        || ws_spec.starts_with("./")
-        || ws_spec.starts_with("../")
-        || ws_spec.starts_with(r".\")
-        || ws_spec.starts_with(r"..\")
-}
-
-fn reached_workspace_project_dirs(
-    check: &OptimisticRepeatInstallCheck<'_>,
-    state: &WorkspaceState,
-    roots: &[&Path],
-) -> HashSet<PathBuf> {
-    let index = WorkspaceProjectIndex::from_check(check);
-    let groups = [
-        (state.settings.production != Some(false)).then_some(DependencyGroup::Prod),
-        (state.settings.dev != Some(false)).then_some(DependencyGroup::Dev),
-        (state.settings.optional != Some(false)).then_some(DependencyGroup::Optional),
-        (check.config.auto_install_peers && state.settings.auto_install_peers != Some(false))
-            .then_some(DependencyGroup::Peer),
-    ];
-    let mut reached = HashSet::new();
-    let mut stack: Vec<PathBuf> = roots
-        .iter()
-        .map(|dir| lexical_normalize(dir))
-        .collect();
-    while let Some(dir) = stack.pop() {
-        let Some(&manifest) = index.by_dir
-            .get(&dir)
-            .filter(|_| reached.insert(dir.clone()))
-        else {
-            continue;
-        };
-        for (alias, spec) in manifest.dependencies(groups.into_iter().flatten()) {
-            stack.extend(index.dep_targets(&dir, alias, spec));
-        }
-    }
-    reached
-}
-
-fn workspace_version_matches_range(version: Option<&str>, range: &str, is_workspace: bool) -> bool {
-    if matches!(range, "" | "*" | "^" | "~") {
-        return true;
-    }
-    if range.parse::<node_semver::Range>().is_err() {
-        return is_workspace;
-    }
-    let Some(version) = version else {
-        return is_workspace;
-    };
-    let parsed_range = IncludePrereleaseRange::parse(range);
-    version == range
-        || version
-            .parse::<node_semver::Version>()
-            .is_ok_and(|parsed| parsed_range.satisfies(&parsed))
-}
 /// The first project that needs a modules directory and lacks one, over the
 /// projects `is_selected` accepts.
 fn first_missing_modules_dir(
diff --git a/pnpm/crates/package-manager/src/optimistic_repeat_install/modules_dirs/workspace_deps.rs b/pnpm/crates/package-manager/src/optimistic_repeat_install/modules_dirs/workspace_deps.rs
new file mode 100644
index 0000000000..6cb7ed99f2
--- /dev/null
+++ b/pnpm/crates/package-manager/src/optimistic_repeat_install/modules_dirs/workspace_deps.rs
@@ -0,0 +1,183 @@
+use crate::optimistic_repeat_install::{
+    CatalogAnchor, CatalogResolutionResult, Catalogs, OptimisticRepeatInstallCheck,
+    WantedDependency, manifest_string_field, resolve_from_catalog,
+};
+use pnpm_fs::lexical_normalize;
+use pnpm_package_manifest::{DependencyGroup, PackageManifest};
+use pnpm_semver_include_prerelease::IncludePrereleaseRange;
+use pnpm_workspace_state::WorkspaceState;
+use std::{
+    borrow::Cow,
+    collections::{HashMap, HashSet},
+    path::{Path, PathBuf},
+};
+
+struct WorkspaceProjectIndex<'a> {
+    workspace_dir: PathBuf,
+    by_dir: HashMap<PathBuf, &'a PackageManifest>,
+    by_name: HashMap<String, Vec<(PathBuf, Option<String>)>>,
+    link_workspace_packages: bool,
+    only_link_deps: bool,
+    catalogs: &'a Catalogs,
+}
+
+impl<'a> WorkspaceProjectIndex<'a> {
+    fn from_check(check: &OptimisticRepeatInstallCheck<'a>) -> Self {
+        let mut by_dir = HashMap::new();
+        let mut by_name: HashMap<String, Vec<(PathBuf, Option<String>)>> = HashMap::new();
+        for (dir, manifest) in check.project_manifests {
+            let norm = lexical_normalize(dir);
+            by_dir.insert(norm.clone(), *manifest);
+            if let Some(name) = manifest_string_field(manifest, "name") {
+                let version = manifest_string_field(manifest, "version");
+                by_name
+                    .entry(name)
+                    .or_default()
+                    .push((norm, version));
+            }
+        }
+        // Where `pnpm-workspace.yaml` sits, so a local-path catalog entry is
+        // re-anchored from the workspace directory even when `lockfile_dir`
+        // moves `check.workspace_root` elsewhere.
+        let workspace_dir = check.config.workspace_dir
+            .as_deref()
+            .or_else(|| {
+                check.config.lockfile_dir
+                    .is_some()
+                    .then(|| check.project_manifests.first().map(|(dir, _)| dir.as_path()))
+                    .flatten()
+            })
+            .unwrap_or(check.workspace_root);
+        Self {
+            workspace_dir: lexical_normalize(workspace_dir),
+            by_dir,
+            by_name,
+            link_workspace_packages: check.config.link_workspace_packages.enabled_at_depth(0),
+            only_link_deps: !check.config.shares_one_lockfile()
+                && check.config.inject_workspace_packages,
+            catalogs: check.catalogs,
+        }
+    }
+
+    fn dereference_catalog<'b>(
+        &self,
+        dir: &Path,
+        alias: &str,
+        spec: &'b str,
+    ) -> Option<Cow<'b, str>> {
+        if !spec.starts_with("catalog:") {
+            return Some(Cow::Borrowed(spec));
+        }
+        let CatalogResolutionResult::Found(found) = resolve_from_catalog(
+            self.catalogs,
+            &WantedDependency { alias: alias.to_string(), bare_specifier: spec.to_string() },
+            CatalogAnchor::Reanchor { workspace_dir: &self.workspace_dir, consumer_dir: Some(dir) },
+        ) else {
+            return None;
+        };
+        Some(Cow::Owned(found.resolution.specifier))
+    }
+
+    fn dep_targets(&self, dir: &Path, alias: &str, spec: &str) -> Vec<PathBuf> {
+        let Some(spec) = self.dereference_catalog(dir, alias, spec) else {
+            return Vec::new();
+        };
+        let spec = spec.as_ref();
+        if let Some(rel) = spec.strip_prefix("link:") {
+            return self.resolve_dir_target(dir, rel);
+        }
+        if self.only_link_deps {
+            return Vec::new();
+        }
+        if let Some(rel) = spec.strip_prefix("file:") {
+            return self.resolve_dir_target(dir, rel);
+        }
+        let is_workspace = spec.starts_with("workspace:");
+        if !is_workspace && !self.link_workspace_packages {
+            return Vec::new();
+        }
+        if let Some(ws_spec) = spec.strip_prefix("workspace:")
+            && is_relative_workspace_path(ws_spec)
+        {
+            return self.resolve_dir_target(dir, ws_spec);
+        }
+        let (target_name, range) = crate::install::spec_target_and_range(spec);
+        let name = target_name.unwrap_or(alias);
+        self.by_name
+            .get(name)
+            .into_iter()
+            .flatten()
+            .filter(|(_, version)| {
+                workspace_version_matches_range(version.as_deref(), range, is_workspace)
+            })
+            .map(|(dir, _)| dir.clone())
+            .collect()
+    }
+
+    fn resolve_dir_target(&self, dir: &Path, rel: &str) -> Vec<PathBuf> {
+        let normalized_rel = rel.replace('\\', "/");
+        let target = lexical_normalize(&dir.join(normalized_rel));
+        self.by_dir
+            .contains_key(&target)
+            .then_some(target)
+            .into_iter()
+            .collect()
+    }
+}
+
+fn is_relative_workspace_path(ws_spec: &str) -> bool {
+    matches!(ws_spec, "." | "..")
+        || ws_spec.starts_with("./")
+        || ws_spec.starts_with("../")
+        || ws_spec.starts_with(r".\")
+        || ws_spec.starts_with(r"..\")
+}
+
+pub(super) fn reached_workspace_project_dirs(
+    check: &OptimisticRepeatInstallCheck<'_>,
+    state: &WorkspaceState,
+    roots: &[&Path],
+) -> HashSet<PathBuf> {
+    let index = WorkspaceProjectIndex::from_check(check);
+    let groups = [
+        (state.settings.production != Some(false)).then_some(DependencyGroup::Prod),
+        (state.settings.dev != Some(false)).then_some(DependencyGroup::Dev),
+        (state.settings.optional != Some(false)).then_some(DependencyGroup::Optional),
+        (check.config.auto_install_peers && state.settings.auto_install_peers != Some(false))
+            .then_some(DependencyGroup::Peer),
+    ];
+    let mut reached = HashSet::new();
+    let mut stack: Vec<PathBuf> = roots
+        .iter()
+        .map(|dir| lexical_normalize(dir))
+        .collect();
+    while let Some(dir) = stack.pop() {
+        let Some(&manifest) = index.by_dir
+            .get(&dir)
+            .filter(|_| reached.insert(dir.clone()))
+        else {
+            continue;
+        };
+        for (alias, spec) in manifest.dependencies(groups.into_iter().flatten()) {
+            stack.extend(index.dep_targets(&dir, alias, spec));
+        }
+    }
+    reached
+}
+
+fn workspace_version_matches_range(version: Option<&str>, range: &str, is_workspace: bool) -> bool {
+    if matches!(range, "" | "*" | "^" | "~") {
+        return true;
+    }
+    if range.parse::<node_semver::Range>().is_err() {
+        return is_workspace;
+    }
+    let Some(version) = version else {
+        return is_workspace;
+    };
+    let parsed_range = IncludePrereleaseRange::parse(range);
+    version == range
+        || version
+            .parse::<node_semver::Version>()
+            .is_ok_and(|parsed| parsed_range.satisfies(&parsed))
+}
diff --git a/pnpm/crates/package-manager/src/optimistic_repeat_install/tests/catalogs.rs b/pnpm/crates/package-manager/src/optimistic_repeat_install/tests/catalogs.rs
index 5b8b1f9ec1..b8ca7e0eff 100644
--- a/pnpm/crates/package-manager/src/optimistic_repeat_install/tests/catalogs.rs
+++ b/pnpm/crates/package-manager/src/optimistic_repeat_install/tests/catalogs.rs
@@ -251,3 +251,67 @@ fn returns_outdated_when_single_project_catalog_cache_changes() {
     );
     assert_eq!(decision, Decision::Skipped { reason: "catalogs cache outdated" });
 }
+
+#[test]
+fn expanded_selected_modules_dir_check_reanchors_catalog_links_from_workspace_dir_not_lockfile_dir()
+{
+    let linker = pnpm_config::NodeLinker::Isolated;
+    let external_lockfile_dir = tempdir().unwrap();
+    let (dir, config, root_manifest) = setup_fresh_install_with_config(
+        linker,
+        "root",
+        "1.0.0",
+        r#""dependencies":{"linked":"catalog:"}"#,
+        |config| {
+            config.lockfile_dir = Some(external_lockfile_dir.path().to_path_buf());
+        },
+    );
+    let linked_dir = dir.path().join("packages/linked");
+    fs::create_dir_all(&linked_dir).unwrap();
+    let linked_manifest_path = linked_dir.join("package.json");
+    fs::write(
+        &linked_manifest_path,
+        r#"{"name":"linked","version":"1.0.0","dependencies":{"foo":"1.0.0"}}"#,
+    )
+    .unwrap();
+    let linked_manifest = PackageManifest::from_path(linked_manifest_path).unwrap();
+
+    let project_manifests =
+        [(dir.path().to_path_buf(), &root_manifest), (linked_dir.clone(), &linked_manifest)];
+    let catalogs = BTreeMap::from([(
+        "default".to_string(),
+        BTreeMap::from([("linked".to_string(), "link:./packages/linked".to_string())]),
+    )]);
+    let check = OptimisticRepeatInstallCheck {
+        workspace_root: external_lockfile_dir.path(),
+        config,
+        project_manifests: &project_manifests,
+        is_workspace_install: true,
+        lockfile: MaybeLazyLockfile::Loaded(None),
+        catalogs: &catalogs,
+        layout: crate::RepeatInstallLayout {
+            node_linker: linker,
+            included: isolated_included(),
+            supported_architectures: None,
+        },
+        manifests: crate::RepeatInstallManifests::ON_DISK,
+    };
+    let state = pnpm_workspace_state::WorkspaceState::default();
+    let selected = [dir.path()];
+
+    assert_eq!(
+        super::super::modules_dirs::first_selected_project_missing_modules_dir(
+            &check, &state, &selected, true,
+        )
+        .as_deref(),
+        Some("linked"),
+    );
+
+    fs::create_dir_all(linked_dir.join("node_modules")).unwrap();
+    assert_eq!(
+        super::super::modules_dirs::first_selected_project_missing_modules_dir(
+            &check, &state, &selected, true,
+        ),
+        None,
+    );
+}
diff --git a/pnpm/crates/package-manager/src/optimistic_repeat_install/tests/modules_dir.rs b/pnpm/crates/package-manager/src/optimistic_repeat_install/tests/modules_dir.rs
index f1d559195d..405e4d2229 100644
--- a/pnpm/crates/package-manager/src/optimistic_repeat_install/tests/modules_dir.rs
+++ b/pnpm/crates/package-manager/src/optimistic_repeat_install/tests/modules_dir.rs
@@ -408,3 +408,79 @@ fn expanded_selected_modules_dir_check_follows_aliases_paths_and_matching_versio
         Some("pkg-f"),
     );
 }
+
+#[test]
+fn expanded_selected_modules_dir_check_under_dedicated_lockfiles_with_injection_follows_only_link_deps()
+ {
+    let linker = pnpm_config::NodeLinker::Isolated;
+    let (dir, config, root_manifest) =
+        setup_fresh_install_with_config(linker, "root", "1.0.0", "", |config| {
+            config.shared_workspace_lockfile = false;
+            config.inject_workspace_packages = true;
+        });
+    let write_pkg = |rel: &str, json: &str, create_modules_dir: bool| {
+        let pkg_dir = dir.path().join(rel);
+        fs::create_dir_all(&pkg_dir).unwrap();
+        if create_modules_dir {
+            fs::create_dir_all(pkg_dir.join("node_modules")).unwrap();
+        }
+        let manifest_path = pkg_dir.join("package.json");
+        fs::write(&manifest_path, json).unwrap();
+        (pkg_dir, PackageManifest::from_path(manifest_path).unwrap())
+    };
+    let (app_dir, app_manifest) = write_pkg(
+        "app",
+        r#"{"name":"app","version":"1.0.0","dependencies":{"injected":"workspace:*","linked":"link:../linked"}}"#,
+        true,
+    );
+    let (injected_dir, injected_manifest) = write_pkg(
+        "injected",
+        r#"{"name":"injected","version":"1.0.0","dependencies":{"foo":"1.0.0"}}"#,
+        false,
+    );
+    let (linked_dir, linked_manifest) = write_pkg(
+        "linked",
+        r#"{"name":"linked","version":"1.0.0","dependencies":{"foo":"1.0.0"}}"#,
+        false,
+    );
+
+    let project_manifests = [
+        (dir.path().to_path_buf(), &root_manifest),
+        (app_dir.clone(), &app_manifest),
+        (injected_dir, &injected_manifest),
+        (linked_dir.clone(), &linked_manifest),
+    ];
+    let catalogs = BTreeMap::default();
+    let check = OptimisticRepeatInstallCheck {
+        workspace_root: dir.path(),
+        config,
+        project_manifests: &project_manifests,
+        is_workspace_install: true,
+        lockfile: MaybeLazyLockfile::Loaded(None),
+        catalogs: &catalogs,
+        layout: crate::RepeatInstallLayout {
+            node_linker: linker,
+            included: isolated_included(),
+            supported_architectures: None,
+        },
+        manifests: crate::RepeatInstallManifests::ON_DISK,
+    };
+    let state = pnpm_workspace_state::WorkspaceState::default();
+    let selected = [app_dir.as_path()];
+
+    assert_eq!(
+        super::super::modules_dirs::first_selected_project_missing_modules_dir(
+            &check, &state, &selected, true,
+        )
+        .as_deref(),
+        Some("linked"),
+    );
+
+    fs::create_dir_all(linked_dir.join("node_modules")).unwrap();
+    assert_eq!(
+        super::super::modules_dirs::first_selected_project_missing_modules_dir(
+            &check, &state, &selected, true,
+        ),
+        None,
+    );
+}
diff --git a/pnpm11/__fixtures__/pnpm-workspace.yaml b/pnpm11/__fixtures__/pnpm-workspace.yaml
index fea4dd5fb4..c1668526b4 100644
--- a/pnpm11/__fixtures__/pnpm-workspace.yaml
+++ b/pnpm11/__fixtures__/pnpm-workspace.yaml
@@ -14,6 +14,7 @@ packages:
   - '!has-yarn2-lock'
   - '!workspace-with-lockfile-dupes'
   - '!workspace-with-lockfile-subdep-dupes'
+  - '!workspace-with-nested-workspace-deps'
   - '!workspace-has-shared-yarn-lock'
   - '!workspace-has-shared-package-lock-json'
   - '!workspace-has-shared-npm-shrinkwrap-json'
diff --git a/pnpm11/deps/status/test/recordedValidation.test.ts b/pnpm11/deps/status/test/recordedValidation.test.ts
index 3374889f93..d4322d9e28 100644
--- a/pnpm11/deps/status/test/recordedValidation.test.ts
+++ b/pnpm11/deps/status/test/recordedValidation.test.ts
@@ -486,6 +486,45 @@ describe('checkDepsStatus with recorded validations', () => {
     await fs.mkdir(bLockfilePath)
     await fs.utimes(bLockfilePath, bLockfileMtime, bLockfileMtime)
     expect(await check(workspace, ['a'], { sharedWorkspaceLockfile: false })).toMatchObject({ upToDate: true })
+
+    // Under dedicated lockfiles with injection, a non-recursive check in `a`
+    // skips injected `workspace:*` dependencies while still holding `link:` dependencies.
+    await fs.rm(bLockfilePath, { recursive: true, force: true })
+    await fs.rm(path.join(workspace.projectDir('b'), 'node_modules'), { recursive: true, force: true })
+    const recordVouchedA = async (bSpec: string): Promise<void> => {
+      workspace.manifestOf('a').dependencies = { foo: '1.0.0', b: bSpec }
+      await updateWorkspaceState({
+        allProjects: workspace.allProjects,
+        workspaceDir: workspace.workspaceDir,
+        pnpmfiles: [],
+        settings: { ...SETTINGS, injectWorkspacePackages: true },
+        configDependencies: CONFIG_DEPENDENCIES,
+        filteredInstall: true,
+        validation: {
+          lockfileDir: workspace.workspaceDir,
+          wantedLockfileName: 'pnpm-lock.yaml',
+          sharedInputs: [],
+          sharedWorkspaceLockfile: false,
+          vouchedProjects: [workspace.projectDir('a')],
+        },
+      })
+    }
+    await recordVouchedA('workspace:*')
+    expect(await check(workspace, undefined, {
+      dir: workspace.projectDir('a'),
+      injectWorkspacePackages: true,
+      sharedWorkspaceLockfile: false,
+    })).toMatchObject({ upToDate: true })
+
+    await recordVouchedA('link:../b')
+    expect(await check(workspace, undefined, {
+      dir: workspace.projectDir('a'),
+      injectWorkspacePackages: true,
+      sharedWorkspaceLockfile: false,
+    })).toMatchObject({
+      upToDate: false,
+      issue: 'Workspace package b has dependencies but does not have a modules directory',
+    })
   })
 })
 
diff --git a/pnpm11/exec/commands/src/selectProjectsToVerify.ts b/pnpm11/exec/commands/src/selectProjectsToVerify.ts
index 809d52fb17..daccd128a4 100644
--- a/pnpm11/exec/commands/src/selectProjectsToVerify.ts
+++ b/pnpm11/exec/commands/src/selectProjectsToVerify.ts
@@ -66,29 +66,27 @@ function walkDependencies (projectsGraph: ProjectsGraph, roots: ProjectRootDir[]
     const node = projectsGraph[dir]
     if (reached[dir] != null || node == null) continue
     reached[dir] = node
-    const dependencies = onlyLinked
-      ? node.dependencies.filter((depDir) => hasLinkDependencyTo(dir, node.package.manifest, depDir))
-      : node.dependencies
+    let dependencies = node.dependencies
+    if (onlyLinked && dependencies.length > 0) {
+      const linkedTargets = linkedDependencyDirs(dir, node.package.manifest)
+      dependencies = dependencies.filter((depDir) => linkedTargets.has(path.resolve(depDir)))
+    }
     stack.push(...dependencies)
   }
   return reached
 }
 
-function hasLinkDependencyTo (parentDir: ProjectRootDir, manifest: ProjectManifest | undefined, targetDir: ProjectRootDir): boolean {
-  if (manifest == null) return false
-  const resolvedTarget = path.resolve(targetDir)
+function linkedDependencyDirs (parentDir: ProjectRootDir, manifest: ProjectManifest | undefined): Set<string> {
+  const targets = new Set<string>()
+  if (manifest == null) return targets
   for (const field of ['dependencies', 'devDependencies', 'optionalDependencies', 'peerDependencies'] as const) {
     for (const spec of Object.values(manifest[field] ?? {})) {
-      if (
-        typeof spec === 'string' &&
-        spec.startsWith('link:') &&
-        path.resolve(parentDir, spec.slice('link:'.length).replace(/\\/g, '/')) === resolvedTarget
-      ) {
-        return true
+      if (typeof spec === 'string' && spec.startsWith('link:')) {
+        targets.add(path.resolve(parentDir, spec.slice('link:'.length).replace(/\\/g, '/')))
       }
     }
   }
-  return false
+  return targets
 }
 
 function hasNegatedSelector (opts: ProjectsToVerifyOptions): boolean {
diff --git a/pnpm11/pnpm/test/verifyDepsBeforeRun/multiProjectWorkspace.ts b/pnpm11/pnpm/test/verifyDepsBeforeRun/multiProjectWorkspace.ts
index b386cc34f4..8d9505be20 100644
--- a/pnpm11/pnpm/test/verifyDepsBeforeRun/multiProjectWorkspace.ts
+++ b/pnpm11/pnpm/test/verifyDepsBeforeRun/multiProjectWorkspace.ts
@@ -1146,6 +1146,80 @@ test('exec installs a workspace dependency of the selected project after a filte
   expect(fs.existsSync(path.resolve('bar/node_modules/@pnpm.e2e/foo'))).toBeTruthy()
 })
 
+// Under dedicated lockfiles with `injectWorkspacePackages`, an injected
+// `workspace:*` dependency is a copy inside the dependent project that its own
+// install covers, whereas an explicit `link:` dependency remains a symlink
+// whose target project must still be installed
+// (https://github.com/pnpm/tasks/issues/179).
+test('exec holds a link: dependency under dedicated lockfiles with injectWorkspacePackages', async () => {
+  const projects = preparePackages([
+    {
+      location: '.',
+      package: { name: 'root', private: true },
+    },
+    {
+      name: 'foo',
+      private: true,
+      dependencies: { bar: 'workspace:*' },
+    },
+    {
+      name: 'bar',
+      private: true,
+      dependencies: { '@pnpm.e2e/foo': '=100.0.0' },
+    },
+    {
+      name: 'baz',
+      private: true,
+      dependencies: { '@pnpm.e2e/foo': '=100.0.0' },
+    },
+  ])
+  writeYamlFileSync('pnpm-workspace.yaml', {
+    packages: ['**', '!store/**'],
+    sharedWorkspaceLockfile: false,
+    injectWorkspacePackages: true,
+  })
+
+  execPnpmSync(['--filter=foo', 'install'], { expectSuccess: true })
+  expect(fs.existsSync(path.resolve('bar/node_modules'))).toBeFalsy()
+
+  const injectedResult = execPnpmSync([
+    ...CONFIG,
+    '--filter=foo',
+    'exec',
+    'node',
+    '-e',
+    "console.log('injected-ok')",
+  ], { expectSuccess: true })
+  expect(injectedResult.stdout.toString()).toContain('injected-ok')
+
+  projects.foo.writePackageJson({
+    name: 'foo',
+    private: true,
+    dependencies: {
+      bar: 'workspace:*',
+      baz: 'link:../baz',
+    },
+  })
+  execPnpmSync(['--filter=foo', 'install'], { expectSuccess: true })
+  expect(fs.existsSync(path.resolve('baz/node_modules'))).toBeFalsy()
+
+  const { status, stdout } = execPnpmSync([...CONFIG, '--filter=foo', 'exec', 'node', '-e', '0'])
+  expect(status).not.toBe(0)
+  expect(stdout.toString()).toContain('ERR_PNPM_VERIFY_DEPS_BEFORE_RUN')
+
+  const linkedResult = execPnpmSync([
+    '--config.verify-deps-before-run=install',
+    '--filter=foo',
+    'exec',
+    'node',
+    '-e',
+    "console.log('linked-ok')",
+  ], { expectSuccess: true })
+  expect(linkedResult.stdout.toString()).toContain('linked-ok')
+  expect(fs.existsSync(path.resolve('baz/node_modules/@pnpm.e2e/foo'))).toBeTruthy()
+  execPnpmSync([...CONFIG, '--filter=foo', 'exec', 'node', '-e', '0'], { expectSuccess: true })
+})
+
 // A negated selector reaches the install the gate spawns unchanged, so the
 // project it excludes is not required to have a modules directory.
 test('exec does not require a workspace dependency that a negated selector excludes', async () => {
diff --git a/pnpm11/workspace/projects-graph/src/index.ts b/pnpm11/workspace/projects-graph/src/index.ts
index 6028924b35..4a61603022 100644
--- a/pnpm11/workspace/projects-graph/src/index.ts
+++ b/pnpm11/workspace/projects-graph/src/index.ts
@@ -104,6 +104,7 @@ function parseDependencySpec (
   isWorkspaceSpec: boolean
 ): { depName: string, rawSpec: string, spec: { fetchSpec: string, type: string } } | undefined {
   try {
+    const isLinkSpec = !isWorkspaceSpec && rawSpec.startsWith('link:')
     if (isWorkspaceSpec) {
       const npmSpec = workspacePrefToNpm(rawSpec)
       if (isRelativePathSpec(npmSpec)) {
@@ -113,8 +114,13 @@ function parseDependencySpec (
       }
     } else if (rawSpec.startsWith('npm:')) {
       ({ depName, rawSpec } = parseRegistrySpec(depName, rawSpec))
+    } else if (isLinkSpec) {
+      rawSpec = `file:${rawSpec.slice('link:'.length)}`
     }
     const spec = npa.resolve(depName, rawSpec, projectRootDir)
+    if (isLinkSpec && spec.type === 'file') {
+      spec.type = 'directory'
+    }
     return { depName, rawSpec, spec }
   } catch {
     return undefined
diff --git a/pnpm11/workspace/projects-graph/test/index.ts b/pnpm11/workspace/projects-graph/test/index.ts
index f85be3a2ee..b4ea99f3c5 100644
--- a/pnpm11/workspace/projects-graph/test/index.ts
+++ b/pnpm11/workspace/projects-graph/test/index.ts
@@ -166,6 +166,7 @@ test('create package graph using peer dependencies', () => {
 })
 
 test('create package graph for local directory dependencies', () => {
+  const TAR_DIR_PATH = pathResolve('/zkochan/src/bar.tgz')
   const result = createProjectsGraph([
     {
       rootDir: BAR1_PATH,
@@ -199,9 +200,18 @@ test('create package graph for local directory dependencies', () => {
 
         dependencies: {
           foo: 'file:../foo@2',
+          bar1: 'link:../bar',
+          tarDir: 'link:../bar.tgz',
         },
       },
     },
+    {
+      rootDir: TAR_DIR_PATH,
+      manifest: {
+        name: 'tar-dir',
+        version: '1.0.0',
+      },
+    },
     {
       rootDir: FOO2_PATH,
       manifest: {
@@ -243,7 +253,7 @@ test('create package graph for local directory dependencies', () => {
       },
     },
     [BAR2_PATH]: {
-      dependencies: [FOO2_PATH],
+      dependencies: [FOO2_PATH, BAR1_PATH, TAR_DIR_PATH],
       package: {
         rootDir: BAR2_PATH,
         manifest: {
@@ -252,10 +262,22 @@ test('create package graph for local directory dependencies', () => {
 
           dependencies: {
             foo: 'file:../foo@2',
+            bar1: 'link:../bar',
+            tarDir: 'link:../bar.tgz',
           },
         },
       },
     },
+    [TAR_DIR_PATH]: {
+      dependencies: [],
+      package: {
+        rootDir: TAR_DIR_PATH,
+        manifest: {
+          name: 'tar-dir',
+          version: '1.0.0',
+        },
+      },
+    },
     [FOO2_PATH]: {
       dependencies: [],
       package: {