diff --git a/scanner/tag_scanner.go b/scanner/tag_scanner.go
index 6bd654ece..43df122da 100644
--- a/scanner/tag_scanner.go
+++ b/scanner/tag_scanner.go
@@ -75,6 +75,16 @@ func (s *TagScanner) Scan(ctx context.Context, lastModifiedSince time.Time, prog
 	// Special case: if lastModifiedSince is zero, re-import all files
 	fullScan := lastModifiedSince.IsZero()
 
+	// If the media folder is empty (no music and no subfolders), abort to avoid deleting all data from DB
+	empty, err := isDirEmpty(ctx, s.rootFolder)
+	if err != nil {
+		return 0, err
+	}
+	if empty && !fullScan {
+		log.Error(ctx, "Media Folder is empty. Aborting scan.", "folder", s.rootFolder)
+		return 0, nil
+	}
+
 	allDBDirs, err := s.getDBDirTree(ctx)
 	if err != nil {
 		return 0, err
@@ -110,12 +120,6 @@ func (s *TagScanner) Scan(ctx context.Context, lastModifiedSince time.Time, prog
 		return 0, err
 	}
 
-	// If the media folder is empty, abort to avoid deleting all data
-	if len(allFSDirs) <= 1 {
-		log.Error(ctx, "Media Folder is empty. Aborting scan.", "folder", s.rootFolder)
-		return 0, nil
-	}
-
 	deletedDirs := s.getDeletedDirs(ctx, allFSDirs, allDBDirs)
 	if len(deletedDirs)+len(changedDirs) == 0 {
 		log.Debug(ctx, "No changes found in Music Folder", "folder", s.rootFolder, "elapsed", time.Since(start))
@@ -155,6 +159,11 @@ func (s *TagScanner) Scan(ctx context.Context, lastModifiedSince time.Time, prog
 	return s.cnt.total(), err
 }
 
+func isDirEmpty(ctx context.Context, dir string) (bool, error) {
+	children, stats, err := loadDir(ctx, dir)
+	return len(children) == 0 && stats.AudioFilesCount == 0, err
+}
+
 func (s *TagScanner) getRootFolderWalker(ctx context.Context) (walkResults, chan error) {
 	start := time.Now()
 	log.Trace(ctx, "Loading directory tree from music folder", "folder", s.rootFolder)