diff --git a/zuul_registry/storage.py b/zuul_registry/storage.py
index 3492951..2563701 100644
--- a/zuul_registry/storage.py
+++ b/zuul_registry/storage.py
@@ -277,8 +277,9 @@ class Storage:
             if not manifest_target:
                 continue
             repopath = os.path.join(namespace.path, 'repos/')
+            kept_manifests = []
             for repo in self.backend.list_objects(repopath):
-                kept_manifests = self._prune(repo, manifest_target)
+                kept_manifests.extend(self._prune(repo, manifest_target))
             # mark/sweep manifest blobs
             layers = set()
             for manifest in kept_manifests: