diff --git a/storage/local/persistence.go b/storage/local/persistence.go
index d964d4ce8..ace58b6d9 100644
--- a/storage/local/persistence.go
+++ b/storage/local/persistence.go
@@ -162,7 +162,7 @@ func newPersistence(
 		if err != nil {
 			return nil, err
 		}
-		if len(fis) > 0 {
+		if len(fis) > 0 && !(len(fis) == 1 && fis[0].Name() == "lost+found" && fis[0].IsDir()) {
 			return nil, fmt.Errorf("could not detect storage version on disk, assuming version 0, need version %d - please wipe storage or run a version of Prometheus compatible with storage version 0", Version)
 		}
 		// Finally we can write our own version into a new version file.