diff --git a/rhodecode/lib/cleanup.py b/rhodecode/lib/cleanup.py
--- a/rhodecode/lib/cleanup.py
+++ b/rhodecode/lib/cleanup.py
@@ -88,9 +88,10 @@ class CleanupCommand(BasePasterCommand):
 
         repos_location = RhodeCodeUi.get_repos_location()
         to_remove = []
-        for loc in os.listdir(repos_location):
-            if REMOVED_REPO_PAT.match(loc):
-                to_remove.append([loc, self._extract_date(loc)])
+        for dn, dirs, f in os.walk(str(repos_location)):
+            for loc in dirs:
+                if REMOVED_REPO_PAT.match(loc):
+                    to_remove.append([loc, self._extract_date(loc)])
 
         #filter older than (if present)!
         now = datetime.datetime.now()