diff --git a/registry/storage/vacuum.go b/registry/storage/vacuum.go
index e074b45c9..ff981bb47 100644
--- a/registry/storage/vacuum.go
+++ b/registry/storage/vacuum.go
@@ -91,11 +91,30 @@ func (v Vacuum) RemoveRepository(repoName string) error {
 	if err != nil {
 		return err
 	}
-	repoDir := path.Join(rootForRepository, repoName)
-	dcontext.GetLogger(v.ctx).Infof("Deleting repo: %s", repoDir)
-	err = v.driver.Delete(v.ctx, repoDir)
+	repoManifestDir := path.Join(rootForRepository, repoName, "_manifests")
+	dcontext.GetLogger(v.ctx).Infof("Deleting repo: %s", repoManifestDir)
+	err = v.driver.Delete(v.ctx, repoManifestDir)
 	if err != nil {
-		return err
+		if _, ok := err.(driver.PathNotFoundError); !ok {
+			return err
+		}
+	}
+	repoLayerDir := path.Join(rootForRepository, repoName, "_layers")
+	dcontext.GetLogger(v.ctx).Infof("Deleting repo: %s", repoLayerDir)
+	err = v.driver.Delete(v.ctx, repoLayerDir)
+	if err != nil {
+		if _, ok := err.(driver.PathNotFoundError); !ok {
+			return err
+		}
+	}
+
+	repoUploadDir := path.Join(rootForRepository, repoName, "_uploads")
+	dcontext.GetLogger(v.ctx).Infof("Deleting repo: %s", repoUploadDir)
+	err = v.driver.Delete(v.ctx, repoUploadDir)
+	if err != nil {
+		if _, ok := err.(driver.PathNotFoundError); !ok {
+			return err
+		}
 	}
 
 	return nil