diff --git a/.changeset/hoisted-file-dep-peer-variants-stay-apart.md b/.changeset/hoisted-file-dep-peer-variants-stay-apart.md
new file mode 100644
index 0000000000..493b5a5d43
--- /dev/null
+++ b/.changeset/hoisted-file-dep-peer-variants-stay-apart.md
@@ -0,0 +1,8 @@
+---
+"@pnpm/installing.deps-restorer": patch
+"@pnpm/installing.linking.real-hoist": patch
+"pacquet": patch
+"pnpm": patch
+---
+
+Under `nodeLinker: hoisted`, peer-resolution variants of an injected directory dependency (a `file:` snapshot) are materialized as separate copies again instead of collapsing onto the first-seen variant. Each copy keeps its own peer-resolved dependency set, so a project pinning one peer version no longer resolves another project's variant — Bit root components with conflicting peers across injected copies rely on this.
diff --git a/pnpm/crates/deps-restorer/src/hoisted_dep_graph/tests.rs b/pnpm/crates/deps-restorer/src/hoisted_dep_graph/tests.rs
index 91697d7cc8..9f12d96125 100644
--- a/pnpm/crates/deps-restorer/src/hoisted_dep_graph/tests.rs
+++ b/pnpm/crates/deps-restorer/src/hoisted_dep_graph/tests.rs
@@ -1175,3 +1175,88 @@ fn walker_wires_edges_declared_against_a_collapsed_peer_variant() {
         "a snapshot edge on the collapsed variant resolves to the surviving copy",
     );
 }
+
+/// Peer variants of an injected directory dependency are exempt from
+/// the collapse (see [`pnpm_real_hoist::pkg_id`]), so the walk has to
+/// keep a location — and a direct-dependency entry — per variant,
+/// where every collapsed package funnels into one.
+#[test]
+fn walker_keeps_file_dep_peer_variants_apart() {
+    let mut r1_deps = ResolvedDependencyMap::new();
+    r1_deps.insert(
+        pkg_name("comp"),
+        ResolvedDependencySpec {
+            specifier: "workspace:*".to_string(),
+            version: ver_peer("file:comp(peer@1.0.0)").into(),
+        },
+    );
+    r1_deps.insert(pkg_name("peer"), resolved_dep("1.0.0"));
+    let mut r2_deps = ResolvedDependencyMap::new();
+    r2_deps.insert(
+        pkg_name("comp"),
+        ResolvedDependencySpec {
+            specifier: "workspace:*".to_string(),
+            version: ver_peer("file:comp(peer@2.0.0)").into(),
+        },
+    );
+    r2_deps.insert(pkg_name("peer"), resolved_dep("2.0.0"));
+
+    let mut packages = HashMap::new();
+    packages.insert(
+        dep_key("comp", "file:comp"),
+        PackageMetadata { resolution: directory_resolution("comp"), ..metadata_stub() },
+    );
+    packages.insert(dep_key("peer", "1.0.0"), metadata_stub());
+    packages.insert(dep_key("peer", "2.0.0"), metadata_stub());
+
+    let mut snapshots = HashMap::new();
+    for peer_version in ["1.0.0", "2.0.0"] {
+        let mut comp_deps = HashMap::new();
+        comp_deps.insert(pkg_name("peer"), SnapshotDepRef::Plain(ver_peer(peer_version)));
+        snapshots.insert(
+            dep_key("comp", &format!("file:comp(peer@{peer_version})")),
+            SnapshotEntry { dependencies: Some(comp_deps), ..SnapshotEntry::default() },
+        );
+        snapshots.insert(dep_key("peer", peer_version), SnapshotEntry::default());
+    }
+
+    let lockfile = workspace_lockfile(
+        vec![
+            (Lockfile::ROOT_IMPORTER_KEY, ResolvedDependencyMap::new()),
+            ("node_modules/.bit_roots/r1", r1_deps),
+            ("node_modules/.bit_roots/r2", r2_deps),
+        ],
+        packages,
+        snapshots,
+    );
+    let opts = LockfileToHoistedDepGraphOptions {
+        lockfile_dir: PathBuf::from("/repo"),
+        ..LockfileToHoistedDepGraphOptions::default()
+    };
+    let result = lockfile_to_hoisted_dep_graph(&lockfile, None, &opts).expect("walker succeeds");
+
+    let r1_comp = result.direct_dependencies_by_importer_id["node_modules/.bit_roots/r1"]
+        .get("comp")
+        .expect("r1 keeps its comp direct dependency")
+        .clone();
+    let r2_comp = result.direct_dependencies_by_importer_id["node_modules/.bit_roots/r2"]
+        .get("comp")
+        .expect("r2 keeps its comp direct dependency")
+        .clone();
+    assert_ne!(
+        r1_comp, r2_comp,
+        "each importer's direct dependency must be its own variant's copy",
+    );
+    let r1_peer = result.graph[&r1_comp].children.get("peer").expect("r1's copy resolves peer");
+    let r2_peer = result.graph[&r2_comp].children.get("peer").expect("r2's copy resolves peer");
+    assert_eq!(
+        result.graph[r1_peer].dep_path,
+        DepPath::from("peer@1.0.0".to_string()),
+        "r1's copy must resolve the peer version r1 pinned",
+    );
+    assert_eq!(
+        result.graph[r2_peer].dep_path,
+        DepPath::from("peer@2.0.0".to_string()),
+        "r2's copy must resolve the peer version r2 pinned",
+    );
+}
diff --git a/pnpm/crates/lockfile/src/lib.rs b/pnpm/crates/lockfile/src/lib.rs
index e0390ebd99..67e06e4c4a 100644
--- a/pnpm/crates/lockfile/src/lib.rs
+++ b/pnpm/crates/lockfile/src/lib.rs
@@ -297,9 +297,12 @@ impl Lockfile {
 }
 
 /// Whether `path` ends in a tarball extension (`.tgz`, `.tar.gz`, or
-/// `.tar`, case-insensitively), so the directory-vs-tarball boundary
-/// applied here matches the resolver's at resolve time.
-fn is_local_tarball_path(path: &str) -> bool {
+/// `.tar`, case-insensitively) — the directory-vs-tarball boundary the
+/// resolver applies to a `file:` spec at resolve time. Public so
+/// consumers classifying a `file:` snapshot key (such as the hoister's
+/// identity function) draw the same line.
+#[must_use]
+pub fn is_local_tarball_path(path: &str) -> bool {
     let lower = path.as_bytes();
     let ends_with_ci = |suffix: &str| {
         let bytes = suffix.as_bytes();
diff --git a/pnpm/crates/real-hoist/src/lib.rs b/pnpm/crates/real-hoist/src/lib.rs
index 5a6016f43e..d8b42bbeca 100644
--- a/pnpm/crates/real-hoist/src/lib.rs
+++ b/pnpm/crates/real-hoist/src/lib.rs
@@ -40,7 +40,9 @@
 use derive_more::{Display, Error};
 use indexmap::{IndexMap, IndexSet};
 use miette::Diagnostic;
-use pnpm_lockfile::{Lockfile, PkgName, PkgNameVerPeer, ProjectSnapshot, SnapshotEntry};
+use pnpm_lockfile::{
+    Lockfile, PkgName, PkgNameVerPeer, ProjectSnapshot, SnapshotEntry, VersionPart,
+};
 use std::{
     cell::{Cell, RefCell},
     collections::{BTreeMap, BTreeSet, HashMap, HashSet, VecDeque},
@@ -605,8 +607,27 @@ fn collect_snapshot_deps(
 /// package under a second name gets a node, and a directory, of its
 /// own. An index over the result holds the list and resolves an edge
 /// to its first entry.
+///
+/// An injected directory dependency (a `file:` version that is not a
+/// local tarball) keeps its peer suffix: every variant of it is a
+/// separate on-disk copy of the local package, materialized with its
+/// own peer-resolved dependency set, so collapsing the variants would
+/// rewire every dependent of the losing one onto the survivor's
+/// children (Bit's root components pin conflicting peers across such
+/// copies on purpose). The registry collapse exists to stop
+/// peer-variant explosion on large lockfiles; directory snapshots are
+/// one per injected workspace package and cannot explode that way. A
+/// local tarball (`file:foo.tgz`) unpacks the same archive for every
+/// variant like a registry package, so it collapses like one — the
+/// boundary is [`pnpm_lockfile::is_local_tarball_path`], the same one
+/// the lockfile itself draws for `file:` resolutions.
 #[must_use]
 pub fn pkg_id(dep_key: &PkgNameVerPeer) -> String {
+    if let VersionPart::File(path) = dep_key.suffix.version()
+        && !pnpm_lockfile::is_local_tarball_path(path)
+    {
+        return dep_key.to_string();
+    }
     dep_key.without_peer().to_string()
 }
 
diff --git a/pnpm/crates/real-hoist/src/tests.rs b/pnpm/crates/real-hoist/src/tests.rs
index ae260f05f5..5bd7948f69 100644
--- a/pnpm/crates/real-hoist/src/tests.rs
+++ b/pnpm/crates/real-hoist/src/tests.rs
@@ -1,5 +1,6 @@
 use super::{
-    HoistError, HoistOpts, HoisterResult, RcByPtr, build_hoist_ident_map, hoist, is_preferred_ident,
+    HoistError, HoistOpts, HoisterResult, RcByPtr, build_hoist_ident_map, hoist,
+    is_preferred_ident, percent_encode_path,
 };
 use indexmap::IndexSet;
 use pnpm_lockfile::{
@@ -1316,6 +1317,131 @@ fn peer_suffix_variants_collapse_to_one_hoisted_copy() {
     );
 }
 
+/// Peer variants of an injected directory dependency are exempt from
+/// the collapse — see [`pkg_id`] for why. The fixture mirrors the
+/// teambit/bit root-components layout that caught the regression: two
+/// importers on the same `file:` package, pinning conflicting peers.
+#[test]
+fn file_dep_peer_variants_keep_their_own_copies() {
+    let mut importers = HashMap::new();
+    importers.insert(Lockfile::ROOT_IMPORTER_KEY.to_string(), ProjectSnapshot::default());
+    for (importer_id, peer_ver) in
+        [("node_modules/.bit_roots/r1", "1.0.0"), ("node_modules/.bit_roots/r2", "2.0.0")]
+    {
+        let mut deps = ResolvedDependencyMap::new();
+        deps.insert(
+            pkg_name("comp"),
+            ResolvedDependencySpec {
+                specifier: "workspace:*".to_string(),
+                version: ver_peer(&format!("file:comp(p@{peer_ver})")).into(),
+            },
+        );
+        deps.insert(pkg_name("p"), resolved_dep(peer_ver));
+        importers.insert(
+            importer_id.to_string(),
+            ProjectSnapshot { dependencies: Some(deps), ..ProjectSnapshot::default() },
+        );
+    }
+
+    let mut snapshots = HashMap::new();
+    for peer_ver in ["1.0.0", "2.0.0"] {
+        let mut comp_deps = HashMap::new();
+        comp_deps.insert(pkg_name("p"), SnapshotDepRef::Plain(ver_peer(peer_ver)));
+        snapshots.insert(
+            dep_key("comp", &format!("file:comp(p@{peer_ver})")),
+            SnapshotEntry { dependencies: Some(comp_deps), ..SnapshotEntry::default() },
+        );
+        snapshots.insert(dep_key("p", peer_ver), SnapshotEntry::default());
+    }
+
+    let lockfile = Lockfile { importers, snapshots: Some(snapshots), ..empty_lockfile() };
+
+    let result =
+        hoist(&lockfile, &HoistOpts::default()).expect("file-variant hoist should succeed");
+
+    // Node resolution walks up from the importer, so the copy an
+    // importer sees is the one nested in its own subtree — or the
+    // root's, when its variant was hoisted there. Either placement is
+    // correct only if the reference reached this way is the variant
+    // the importer declared.
+    let root_children = result.dependencies.borrow();
+    let comp_reference_seen_by = |importer: &str| -> String {
+        let importer_name = percent_encode_path(importer);
+        let importer_node =
+            &root_children.iter().find(|dep| dep.0.name == importer_name).unwrap().0;
+        let importer_children = importer_node.dependencies.borrow();
+        let comp = importer_children
+            .iter()
+            .find(|dep| dep.0.name == "comp")
+            .or_else(|| root_children.iter().find(|dep| dep.0.name == "comp"))
+            .unwrap_or_else(|| panic!("no comp reachable from {importer}"));
+        comp.0.references.borrow().iter().next().cloned().unwrap_or_default()
+    };
+    assert_eq!(
+        comp_reference_seen_by("node_modules/.bit_roots/r1"),
+        "comp@file:comp(p@1.0.0)",
+        "r1 must resolve the copy carrying its own peer variant",
+    );
+    assert_eq!(
+        comp_reference_seen_by("node_modules/.bit_roots/r2"),
+        "comp@file:comp(p@2.0.0)",
+        "r2 must resolve the copy carrying its own peer variant",
+    );
+}
+
+/// The directory exemption in [`pkg_id`] must not widen to local
+/// tarballs: a `file:*.tgz` dependency collapses its peer variants
+/// like a registry package.
+#[test]
+fn file_tarball_peer_variants_collapse_like_registry_packages() {
+    let mut importers = HashMap::new();
+    importers.insert(Lockfile::ROOT_IMPORTER_KEY.to_string(), ProjectSnapshot::default());
+    for (importer_id, peer_ver) in [("packages/a", "1.0.0"), ("packages/b", "2.0.0")] {
+        let mut deps = ResolvedDependencyMap::new();
+        deps.insert(
+            pkg_name("tarpkg"),
+            ResolvedDependencySpec {
+                specifier: "file:tarpkg.tgz".to_string(),
+                version: ver_peer(&format!("file:tarpkg.tgz(p@{peer_ver})")).into(),
+            },
+        );
+        deps.insert(pkg_name("p"), resolved_dep(peer_ver));
+        importers.insert(
+            importer_id.to_string(),
+            ProjectSnapshot { dependencies: Some(deps), ..ProjectSnapshot::default() },
+        );
+    }
+
+    let mut snapshots = HashMap::new();
+    for peer_ver in ["1.0.0", "2.0.0"] {
+        let mut tar_deps = HashMap::new();
+        tar_deps.insert(pkg_name("p"), SnapshotDepRef::Plain(ver_peer(peer_ver)));
+        snapshots.insert(
+            dep_key("tarpkg", &format!("file:tarpkg.tgz(p@{peer_ver})")),
+            SnapshotEntry { dependencies: Some(tar_deps), ..SnapshotEntry::default() },
+        );
+        snapshots.insert(dep_key("p", peer_ver), SnapshotEntry::default());
+    }
+
+    let lockfile = Lockfile { importers, snapshots: Some(snapshots), ..empty_lockfile() };
+
+    let result =
+        hoist(&lockfile, &HoistOpts::default()).expect("tarball-variant hoist should succeed");
+    let root_children = result.dependencies.borrow();
+    let tarpkg = &root_children.iter().find(|dep| dep.0.name == "tarpkg").unwrap().0;
+    assert!(
+        tarpkg.references.borrow().contains("tarpkg@file:tarpkg.tgz(p@1.0.0)"),
+        "the first-seen variant is the canonical reference: {tarpkg:#?}",
+    );
+    for importer in ["packages%2Fa", "packages%2Fb"] {
+        let importer_node = &root_children.iter().find(|dep| dep.0.name == importer).unwrap().0;
+        assert!(
+            !importer_node.dependencies.borrow().iter().any(|dep| dep.0.name == "tarpkg"),
+            "a tarball peer variant must dedup against the root copy: {importer_node:#?}",
+        );
+    }
+}
+
 /// A nearer ancestor holding a different version of a name blocks
 /// both hoisting and same-node dedup for that name (upstream's
 /// "filled by parent" scan): removing the edge would make this
diff --git a/pnpm11/installing/deps-restorer/test/lockfileToHoistedDepGraph.test.ts b/pnpm11/installing/deps-restorer/test/lockfileToHoistedDepGraph.test.ts
index 959347c53b..9fa5985eca 100644
--- a/pnpm11/installing/deps-restorer/test/lockfileToHoistedDepGraph.test.ts
+++ b/pnpm11/installing/deps-restorer/test/lockfileToHoistedDepGraph.test.ts
@@ -134,3 +134,57 @@ function peerVariantLockfile (): LockfileObject {
     },
   } as unknown as LockfileObject
 }
+
+// Peer variants of an injected directory dependency are exempt from the
+// collapse (see `getHoisterPkgId`), so the walk has to keep a location
+// per variant, where every collapsed package funnels into one.
+test('lockfileToHoistedDepGraph keeps file-dep peer variants apart', async () => {
+  const dir = tempDir(false)
+  const opts = hoistedOpts(dir)
+  opts.storeController = {
+    fetchPackage: () => ({ filesIndexFile: '' }),
+    getFilesIndexFilePath: () => ({ filesIndexFile: '' }),
+  } as unknown as typeof opts.storeController
+
+  const { graph } = await lockfileToHoistedDepGraph(fileVariantLockfile(), null, opts)
+
+  const compDirs = Object.keys(graph).filter((dir) => path.basename(dir) === 'comp')
+  expect(compDirs).toHaveLength(2)
+  const peerVersionByVariant = Object.fromEntries(compDirs.map((dir) => {
+    const variant = graph[dir].depPath
+    const peerDir = graph[dir].children.peer
+    return [variant, graph[peerDir].depPath]
+  }))
+  expect(peerVersionByVariant).toStrictEqual({
+    'comp@file:comp(peer@1.0.0)': 'peer@1.0.0',
+    'comp@file:comp(peer@2.0.0)': 'peer@2.0.0',
+  })
+})
+
+function fileVariantLockfile (): LockfileObject {
+  const importer = (peerVersion: string) => ({
+    dependencies: {
+      comp: `file:comp(peer@${peerVersion})`,
+      peer: peerVersion,
+    },
+    specifiers: { comp: 'workspace:*', peer: peerVersion },
+  })
+  const compVariant = (peerVersion: string) => ({
+    resolution: { directory: 'comp', type: 'directory' },
+    dependencies: { peer: peerVersion },
+  })
+  return {
+    lockfileVersion: '9.0',
+    importers: {
+      '.': { specifiers: {} },
+      'node_modules/.bit_roots/r1': importer('1.0.0'),
+      'node_modules/.bit_roots/r2': importer('2.0.0'),
+    },
+    packages: {
+      'comp@file:comp(peer@1.0.0)': compVariant('1.0.0'),
+      'comp@file:comp(peer@2.0.0)': compVariant('2.0.0'),
+      'peer@1.0.0': { resolution: { integrity: 'sha512-deadbeef' } },
+      'peer@2.0.0': { resolution: { integrity: 'sha512-deadbeef' } },
+    },
+  } as unknown as LockfileObject
+}
diff --git a/pnpm11/installing/linking/real-hoist/src/index.ts b/pnpm11/installing/linking/real-hoist/src/index.ts
index 505c73e425..f1521ed05d 100644
--- a/pnpm11/installing/linking/real-hoist/src/index.ts
+++ b/pnpm11/installing/linking/real-hoist/src/index.ts
@@ -40,8 +40,25 @@ export type { HoisterResult }
  * `(alias, depPath)`, so an alias exposing a package under a second
  * name gets a node, and a directory, of its own. An index over the
  * result holds the list and resolves an edge to its first entry.
+ *
+ * An injected directory dependency (a `directory` resolution) keeps
+ * its peer suffix: every variant of it is a separate on-disk copy of
+ * the local package, materialized with its own peer-resolved
+ * dependency set, so collapsing the variants would rewire every
+ * dependent of the losing one onto the survivor's children (Bit's
+ * root components pin conflicting peers across such copies on
+ * purpose). The registry collapse exists to stop peer-variant
+ * explosion on large lockfiles; directory snapshots are one per
+ * injected workspace package and cannot explode that way.
  */
 export function getHoisterPkgId (depPath: string, pkgSnapshot: PackageSnapshot): string {
+  // `resolution` is typed as required, but the lockfile is parsed from
+  // untyped YAML — guard so a malformed snapshot degrades to the
+  // collapsed identity instead of a TypeError here.
+  const resolution = pkgSnapshot.resolution as PackageSnapshot['resolution'] | undefined
+  if (resolution != null && 'directory' in resolution && resolution.directory != null) {
+    return depPath
+  }
   const { name, version } = nameVerFromPkgSnapshot(depPath, pkgSnapshot)
   return `${name}@${version}`
 }