diff --git a/.changeset/red-shirts-take.md b/.changeset/red-shirts-take.md
new file mode 100644
index 0000000000..160b694311
--- /dev/null
+++ b/.changeset/red-shirts-take.md
@@ -0,0 +1,5 @@
+---
+"@pnpm/worker": patch
+---
+
+Fix inconsistent store structure due to race condition.
diff --git a/worker/src/start.ts b/worker/src/start.ts
index 33e47cdbac..63011b2317 100644
--- a/worker/src/start.ts
+++ b/worker/src/start.ts
@@ -224,20 +224,25 @@ interface AddFilesFromDirResult {
 
 function initStore ({ storeDir }: InitStoreMessage): { status: string } {
   fs.mkdirSync(storeDir, { recursive: true })
-  try {
-    const hexChars = '0123456789abcdef'.split('')
-    for (const subDir of ['files', 'index']) {
-      const subDirPath = path.join(storeDir, subDir)
+  const hexChars = '0123456789abcdef'.split('')
+  for (const subDir of ['files', 'index']) {
+    const subDirPath = path.join(storeDir, subDir)
+    try {
       fs.mkdirSync(subDirPath)
-      for (const hex1 of hexChars) {
-        for (const hex2 of hexChars) {
+    } catch {
+      // If a parallel process has already started creating the directories in the store,
+      // ignore if it already exists.
+    }
+    for (const hex1 of hexChars) {
+      for (const hex2 of hexChars) {
+        try {
           fs.mkdirSync(path.join(subDirPath, `${hex1}${hex2}`))
+        } catch {
+          // If a parallel process has already started creating the directories in the store,
+          // ignore if it already exists.
         }
       }
     }
-  } catch {
-    // If a parallel process has already started creating the directories in the store,
-    // then we just stop.
   }
   return { status: 'success' }
 }