diff --git a/packages/core/src/config/storageMigration.test.ts b/packages/core/src/config/storageMigration.test.ts
index f95f4a83970..0d2b3796d77 100644
--- a/packages/core/src/config/storageMigration.test.ts
+++ b/packages/core/src/config/storageMigration.test.ts
@@ -64,6 +64,25 @@ describe('StorageMigration', () => {
     expect(fs.existsSync(path.join(newPath, 'old.txt'))).toBe(false);
   });
 
+  it('migrates even if new path contains .project_root (ProjectRegistry initialization)', async () => {
+    const oldPath = path.join(tempDir, 'old-hash');
+    const newPath = path.join(tempDir, 'new-slug');
+    fs.mkdirSync(oldPath);
+    fs.mkdirSync(newPath);
+    fs.writeFileSync(path.join(oldPath, 'history.db'), 'data');
+    fs.writeFileSync(path.join(newPath, '.project_root'), 'path');
+
+    await StorageMigration.migrateDirectory(oldPath, newPath);
+
+    expect(fs.existsSync(path.join(newPath, 'history.db'))).toBe(true);
+    expect(fs.readFileSync(path.join(newPath, 'history.db'), 'utf8')).toBe(
+      'data',
+    );
+    expect(fs.readFileSync(path.join(newPath, '.project_root'), 'utf8')).toBe(
+      'path',
+    );
+  });
+
   it('creates parent directory for new path if it does not exist', async () => {
     const oldPath = path.join(tempDir, 'old-hash');
     const newPath = path.join(tempDir, 'sub', 'new-slug');
diff --git a/packages/core/src/config/storageMigration.ts b/packages/core/src/config/storageMigration.ts
index cc751df38aa..a339741a32e 100644
--- a/packages/core/src/config/storageMigration.ts
+++ b/packages/core/src/config/storageMigration.ts
@@ -22,12 +22,21 @@ export class StorageMigration {
     newPath: string,
   ): Promise<void> {
     try {
-      // If the new path already exists, we consider migration done or skipped to avoid overwriting.
-      // If the old path doesn't exist, there's nothing to migrate.
-      if (fs.existsSync(newPath) || !fs.existsSync(oldPath)) {
+      if (!fs.existsSync(oldPath)) {
         return;
       }
 
+      if (fs.existsSync(newPath)) {
+        const files = await fs.promises.readdir(newPath);
+        // If it contains more than just the .project_root file, it's not a fresh directory from ProjectRegistry
+        if (
+          files.length > 1 ||
+          (files.length === 1 && files[0] !== '.project_root')
+        ) {
+          return;
+        }
+      }
+
       // Ensure the parent directory of the new path exists
       const parentDir = path.dirname(newPath);
       await fs.promises.mkdir(parentDir, { recursive: true });