diff --git a/lib/git-subrepo b/lib/git-subrepo
index eabf9b19..ad05e2ba 100755
--- a/lib/git-subrepo
+++ b/lib/git-subrepo
@@ -1026,6 +1026,11 @@ subrepo:clean() {
         git update-ref -d "$ref"
       fi
     done
+    git show-ref | while read -r hash ref; do
+      if [[ $ref == "refs/original/refs/heads/subrepo/$suffix"* ]]; then
+        git update-ref -d "$ref"
+      fi
+    done
   fi
 }