diff --git a/packages/backend/src/main.test.ts b/packages/backend/src/main.test.ts
index 312f535a..3088a239 100644
--- a/packages/backend/src/main.test.ts
+++ b/packages/backend/src/main.test.ts
@@ -15,6 +15,10 @@ vi.mock('glob', () => ({
     glob: vi.fn().mockReturnValue(['fake_index.zoekt']),
 }));
 
+vi.mock('fs', () => ({
+    existsSync: vi.fn().mockReturnValue(true),
+}));
+
 const createMockContext = (rootPath: string = '/app') => {
     return {
         configPath: path.join(rootPath, 'config.json'),
@@ -159,7 +163,7 @@ test('deleteStaleRepository can delete a git repository', async () => {
 
     await deleteStaleRepository(repo, db, ctx);
 
-    expect(db.data.repos['github.com/sourcebot-dev/sourcebot']).toBeUndefined();;
+    expect(db.data.repos['github.com/sourcebot-dev/sourcebot']).toBeUndefined();
     expect(rm).toHaveBeenCalledWith(`${ctx.reposPath}/github.com/sourcebot-dev/sourcebot`, {
         recursive: true,
     });
diff --git a/packages/backend/src/main.ts b/packages/backend/src/main.ts
index 2942b003..8cb744b2 100644
--- a/packages/backend/src/main.ts
+++ b/packages/backend/src/main.ts
@@ -73,10 +73,10 @@ export const deleteStaleRepository = async (repo: Repository, db: Database, ctx:
     logger.info(`Deleting stale repository ${repo.id}:`);
 
     // Delete the checked out git repository (if applicable)
-    if (repo.vcs === "git") {
+    if (repo.vcs === "git" && existsSync(repo.path)) {
         logger.info(`\tDeleting git directory ${repo.path}...`);
         await rm(repo.path, {
-            recursive: true
+            recursive: true,
         });
     }
 
@@ -116,6 +116,10 @@ export const deleteStaleRepository = async (repo: Repository, db: Database, ctx:
         });
 
         await Promise.all(indexFiles.map((file) => {
+            if (!existsSync(file)) {
+                return;
+            }
+
             logger.info(`\tDeleting index file ${file}...`);
             return rm(file);
         }));