diff --git a/backend/src/index.ts b/backend/src/index.ts
index 798c849d..bc0b50df 100644
--- a/backend/src/index.ts
+++ b/backend/src/index.ts
@@ -10,7 +10,7 @@ import { createIPCServer, type IPCServer } from './ipc/ipcServer'
 import { GitAuthService } from './services/git-auth'
 import { createSettingsRoutes } from './routes/settings'
 import { createHealthRoutes } from './routes/health'
-import { createTTSRoutes, cleanupExpiredCache } from './routes/tts'
+import { createTTSRoutes, cleanupExpiredCache } from './routes/tts';
 import { createSTTRoutes } from './routes/stt'
 import { createFileRoutes } from './routes/files'
 import { createProvidersRoutes } from './routes/providers'
@@ -27,7 +27,6 @@ import { sseAggregator } from './services/sse-aggregator'
 import { ensureDirectoryExists, writeFileContent, fileExists, readFileContent } from './services/file-operations'
 import { SettingsService } from './services/settings'
 import { opencodeServerManager } from './services/opencode-single-server'
-import { cleanupOrphanedDirectories } from './services/repo'
 import { proxyRequest, proxyMcpAuthStart, proxyMcpAuthAuthenticate } from './services/proxy'
 import { NotificationService } from './services/notification'
 import { logger } from './utils/logger'
@@ -181,9 +180,6 @@ try {
   await ensureDirectoryExists(getConfigPath())
   logger.info('Workspace directories initialized')
 
-  await cleanupOrphanedDirectories(db)
-  logger.info('Orphaned directory cleanup completed')
-
   await cleanupExpiredCache()
 
   await ensureDefaultConfigExists()
diff --git a/backend/src/services/repo.ts b/backend/src/services/repo.ts
index 6d15afa9..84cc4abd 100644
--- a/backend/src/services/repo.ts
+++ b/backend/src/services/repo.ts
@@ -710,30 +710,6 @@ function normalizeRepoUrl(url: string, preserveSSH: boolean = false): { url: str
   }
 }
 
-export async function cleanupOrphanedDirectories(database: Database): Promise<void> {
-  try {
-    const reposPath = getReposPath()
-    await ensureDirectoryExists(reposPath)
-
-    const dirResult = await executeCommand(['ls', '-1'], reposPath).catch(() => '')
-    const directories = dirResult.split('\n').filter(d => d.trim())
-
-    if (directories.length === 0) {
-      return
-    }
-
-    const allRepos = db.listRepos(database)
-    const trackedPaths = new Set(allRepos.map(r => r.localPath.split('/').pop()))
-    const orphanedDirs = directories.filter(dir => !trackedPaths.has(dir))
-
-    for (const dir of orphanedDirs) {
-      await executeCommand(['rm', '-rf', dir], reposPath).catch(() => {})
-    }
-  } catch {
-    // Cleanup is best-effort
-  }
-}
-
 async function createWorktreeSafely(baseRepoPath: string, worktreePath: string, branch: string, env: Record<string, string>): Promise<void> {
   const currentBranch = await safeGetCurrentBranch(baseRepoPath, env)
   if (currentBranch === branch) {