diff --git a/internal/backup-vm/handlers/handlers.go b/internal/backup-vm/handlers/handlers.go
index f451461..2b5d4b5 100644
--- a/internal/backup-vm/handlers/handlers.go
+++ b/internal/backup-vm/handlers/handlers.go
@@ -79,6 +79,13 @@ func BackupHandler(w http.ResponseWriter, r *http.Request) {
 	delete := true
 	follow := true
 
+	// Persist empty directories by filling them with .keep file
+	if _, err := s3sync.KeepEmptyDirs(snapPath); err != nil {
+		log.Errorw("error filling empty directories", "error", err)
+		http.Error(w, "failed to persist empty directories", http.StatusInternalServerError)
+		return
+	}
+
 	fmt.Fprintf(w, "Sync snapshot %s into %s\n", createResp.SnapName, bucketPath)
 	syncer := s3sync.New(bucketPath, snapPath, delete, follow)
 	out, err := syncer.Run()
diff --git a/pkg/s3sync/sync.go b/pkg/s3sync/sync.go
index ed29903..96df855 100644
--- a/pkg/s3sync/sync.go
+++ b/pkg/s3sync/sync.go
@@ -42,10 +42,24 @@ func (sc SyncCmd) ComposeCmd() string {
 	return strings.TrimSpace(cmd)
 }
 
+// Run executes composed `aws s3 sync` command.
 func (sc SyncCmd) Run() ([]byte, error) {
+	return runCmd(sc.ComposeCmd())
+}
+
+// KeepEmptyDirs fills empty directories with .keep file.
+// This is useful for syncing empty directories in S3.
+// S3 is an object storage which does not have a concept
+// of the empty directory.
+// https://docs.aws.amazon.com/AmazonS3/latest/dev/UsingMetadata.html
+func KeepEmptyDirs(path string) ([]byte, error) {
+	cmd := fmt.Sprintf("find %s -type d -empty -exec touch {}/.keep \\;", path)
+	return runCmd(cmd)
+}
+
+func runCmd(cmd string) ([]byte, error) {
 	var out []byte
 
-	cmd := sc.ComposeCmd()
 	tokens, err := shlex.Split(cmd)
 	if err != nil {
 		return out, err