diff --git a/.changeset/blue-planes-sort.md b/.changeset/blue-planes-sort.md
new file mode 100644
index 0000000000..39ad9f7a25
--- /dev/null
+++ b/.changeset/blue-planes-sort.md
@@ -0,0 +1,5 @@
+---
+"@pnpm/pkg-manager.direct-dep-linker": patch
+---
+
+Deduping should not fail when node_modules has non-symlinked packages.
diff --git a/pkg-manager/core/test/install/dedupeDirectDeps.ts b/pkg-manager/core/test/install/dedupeDirectDeps.ts
index 5ea2a58dc1..a23718fa5a 100644
--- a/pkg-manager/core/test/install/dedupeDirectDeps.ts
+++ b/pkg-manager/core/test/install/dedupeDirectDeps.ts
@@ -19,6 +19,8 @@ test('dedupe direct dependencies', async () => {
       package: { name: 'project-3' },
     },
   ])
+  fs.mkdirSync('node_modules/foo', { recursive: true })
+  fs.writeFileSync('node_modules/foo/package.json', JSON.stringify({ name: 'foo', version: '1.0.0' }))
 
   const importers: MutatedProject[] = [
     {
@@ -85,6 +87,7 @@ test('dedupe direct dependencies', async () => {
   expect(Array.from(fs.readdirSync('node_modules').sort())).toEqual([
     '.modules.yaml',
     '.pnpm',
+    'foo',
     'is-negative',
     'is-odd',
     'is-positive',
diff --git a/pkg-manager/direct-dep-linker/src/linkDirectDeps.ts b/pkg-manager/direct-dep-linker/src/linkDirectDeps.ts
index d289ac6dc7..6b39d7040f 100644
--- a/pkg-manager/direct-dep-linker/src/linkDirectDeps.ts
+++ b/pkg-manager/direct-dep-linker/src/linkDirectDeps.ts
@@ -71,7 +71,7 @@ function pathsEqual (path1: string, path2: string) {
 async function readLinkedDeps (modulesDir: string): Promise<string[]> {
   const deps = (await readModulesDir(modulesDir)) ?? []
   return Promise.all(
-    deps.map((alias) => resolveLinkTarget(path.join(modulesDir, alias)))
+    deps.map((alias) => resolveLinkTargetOrFile(path.join(modulesDir, alias)))
   )
 }
 
@@ -92,11 +92,20 @@ async function readLinkedDepsWithRealLocations (modulesDir: string) {
     const linkedTo = path.join(modulesDir, alias)
     return {
       linkedTo,
-      linkedFrom: await resolveLinkTarget(linkedTo),
+      linkedFrom: await resolveLinkTargetOrFile(linkedTo),
     }
   }))
 }
 
+async function resolveLinkTargetOrFile (filePath: string) {
+  try {
+    return await resolveLinkTarget(filePath)
+  } catch (err: any) { // eslint-disable-line @typescript-eslint/no-explicit-any
+    if (err.code !== 'EINVAL') throw err
+    return filePath
+  }
+}
+
 async function linkDirectDepsOfProject (project: ProjectToLink) {
   await Promise.all(project.dependencies.map(async (dep) => {
     if (dep.isExternalLink) {