diff --git a/lib/fs/fs.go b/lib/fs/fs.go
index fb05fa876..9e0cefb13 100644
--- a/lib/fs/fs.go
+++ b/lib/fs/fs.go
@@ -186,6 +186,8 @@ func mustSyncParentDirIfExists(path string) {
 
 // MustRemoveAll removes path with all the contents.
 //
+// It properly fsyncs the parent directory after path removal.
+//
 // It properly handles NFS issue https://github.com/VictoriaMetrics/VictoriaMetrics/issues/61 .
 func MustRemoveAll(path string) {
 	_ = mustRemoveAll(path, func() {})
@@ -193,6 +195,8 @@ func MustRemoveAll(path string) {
 
 // MustRemoveAllWithDoneCallback removes path with all the contents.
 //
+// It properly fsyncs the parent directory after path removal.
+//
 // done is called after the path is successfully removed.
 //
 // done may be called after the function returns for NFS path.
diff --git a/lib/storage/partition.go b/lib/storage/partition.go
index 7ed6ca89f..472c532c8 100644
--- a/lib/storage/partition.go
+++ b/lib/storage/partition.go
@@ -240,6 +240,9 @@ func createPartition(timestamp int64, smallPartitionsPath, bigPartitionsPath str
 // The pt must be detached from table before calling pt.Drop.
 func (pt *partition) Drop() {
 	logger.Infof("dropping partition %q at smallPartsPath=%q, bigPartsPath=%q", pt.name, pt.smallPartsPath, pt.bigPartsPath)
+	// Wait until all the pending transaction deletions are finished before removing partition directories.
+	pendingTxnDeletionsWG.Wait()
+
 	fs.MustRemoveAll(pt.smallPartsPath)
 	fs.MustRemoveAll(pt.bigPartsPath)
 	logger.Infof("partition %q has been dropped", pt.name)
@@ -643,6 +646,9 @@ func (pt *partition) PutParts(pws []*partWrapper) {
 func (pt *partition) MustClose() {
 	close(pt.stopCh)
 
+	// Wait until all the pending transaction deletions are finished.
+	pendingTxnDeletionsWG.Wait()
+
 	logger.Infof("waiting for stale parts remover to stop on %q...", pt.smallPartsPath)
 	startTime := time.Now()
 	pt.stalePartsRemoverWG.Wait()
@@ -1352,13 +1358,14 @@ func (pt *partition) removeStaleParts() {
 	pt.snapshotLock.RLock()
 	var removeWG sync.WaitGroup
 	for pw := range m {
-		removeWG.Add(1)
 		logger.Infof("removing part %q, since its data is out of the configured retention (%d secs)", pw.p.path, retentionDeadline/1000)
+		removeWG.Add(1)
 		fs.MustRemoveAllWithDoneCallback(pw.p.path, removeWG.Done)
 	}
 	removeWG.Wait()
-	fs.MustSyncPath(pt.smallPartsPath)
-	fs.MustSyncPath(pt.bigPartsPath)
+	// There is no need in calling fs.MustSyncPath() on pt.smallPartsPath and pt.bigPartsPath,
+	// since they should be automatically called inside fs.MustRemoveAllWithDoneCallback.
+
 	pt.snapshotLock.RUnlock()
 
 	// Remove partition references from removed parts.
@@ -1738,9 +1745,15 @@ func runTransaction(txnLock *sync.RWMutex, pathPrefix1, pathPrefix2, txnPath str
 		}
 	} else {
 		// Just remove srcPath.
-		fs.MustRemoveAll(srcPath)
+		removeWG.Add(1)
+		fs.MustRemoveAllWithDoneCallback(srcPath, removeWG.Done)
 	}
 
+	// Flush pathPrefix* directory metadata to the underying storage,
+	// so the moved files become visible there.
+	fs.MustSyncPath(pathPrefix1)
+	fs.MustSyncPath(pathPrefix2)
+
 	pendingTxnDeletionsWG.Add(1)
 	go func() {
 		defer pendingTxnDeletionsWG.Done()
@@ -1748,9 +1761,9 @@ func runTransaction(txnLock *sync.RWMutex, pathPrefix1, pathPrefix2, txnPath str
 		// This is required for NFS mounts. See https://github.com/VictoriaMetrics/VictoriaMetrics/issues/61 .
 		removeWG.Wait()
 
-		// Flush pathPrefix* directory metadata to the underying storage.
-		fs.MustSyncPath(pathPrefix1)
-		fs.MustSyncPath(pathPrefix2)
+		// There is no need in calling fs.MustSyncPath for pathPrefix* after parts' removal,
+		// since it is already called by fs.MustRemoveAllWithDoneCallback.
+
 		if err := os.Remove(txnPath); err != nil {
 			logger.Errorf("cannot remove transaction file %q: %s", txnPath, err)
 		}