diff --git a/.changeset/great-mayflies-call.md b/.changeset/great-mayflies-call.md
new file mode 100644
index 0000000000..ea3a4654f6
--- /dev/null
+++ b/.changeset/great-mayflies-call.md
@@ -0,0 +1,5 @@
+---
+"@pnpm/package-store": minor
+---
+
+Don't try to create the dependency directory twice.
diff --git a/packages/package-store/src/fs/importIndexedDir.ts b/packages/package-store/src/fs/importIndexedDir.ts
index 1e40d57b57..f8e17b6629 100644
--- a/packages/package-store/src/fs/importIndexedDir.ts
+++ b/packages/package-store/src/fs/importIndexedDir.ts
@@ -44,14 +44,14 @@ async function tryImportIndexedDir (importFile: ImportFile, newDir: string, file
   const alldirs = new Set<string>()
   Object.keys(filenames)
     .forEach((f) => {
-      const dir = path.join(newDir, path.dirname(f))
+      const dir = path.dirname(f)
       if (dir === '.') return
       alldirs.add(dir)
     })
   await Promise.all(
     Array.from(alldirs)
-      .sort((d1, d2) => d1.length - d2.length)
-      .map((dir) => fs.mkdir(dir, { recursive: true }))
+      .sort((d1, d2) => d1.length - d2.length) // from shortest to longest
+      .map((dir) => fs.mkdir(path.join(newDir, dir), { recursive: true }))
   )
   await Promise.all(
     Object.entries(filenames)