diff --git a/lib/mergeset/table.go b/lib/mergeset/table.go
index 10ffdd22dd..edbefa7645 100644
--- a/lib/mergeset/table.go
+++ b/lib/mergeset/table.go
@@ -1062,6 +1062,12 @@ func (tb *Table) CreateSnapshotAt(dstDir string) error {
 }
 
 func runTransactions(txnLock *sync.RWMutex, path string) error {
+	// Wait until all the previous pending transaction deletions are finished.
+	pendingTxnDeletionsWG.Wait()
+
+	// Make sure all the current transaction deletions are finished before exiting.
+	defer pendingTxnDeletionsWG.Wait()
+
 	txnDir := path + "/txn"
 	d, err := os.Open(txnDir)
 	if err != nil {
@@ -1156,7 +1162,9 @@ func runTransaction(txnLock *sync.RWMutex, pathPrefix, txnPath string) error {
 	// Flush pathPrefix directory metadata to the underying storage.
 	fs.MustSyncPath(pathPrefix)
 
+	pendingTxnDeletionsWG.Add(1)
 	go func() {
+		defer pendingTxnDeletionsWG.Done()
 		// Remove the transaction file only after all the source paths are deleted.
 		// This is required for NFS mounts. See https://github.com/VictoriaMetrics/VictoriaMetrics/issues/61 .
 		removeWG.Wait()
@@ -1168,6 +1176,8 @@ func runTransaction(txnLock *sync.RWMutex, pathPrefix, txnPath string) error {
 	return nil
 }
 
+var pendingTxnDeletionsWG syncwg.WaitGroup
+
 func validatePath(pathPrefix, path string) (string, error) {
 	var err error
 
diff --git a/lib/storage/partition.go b/lib/storage/partition.go
index c6b28c6625..39ab6af08e 100644
--- a/lib/storage/partition.go
+++ b/lib/storage/partition.go
@@ -19,6 +19,7 @@ import (
 	"github.com/VictoriaMetrics/VictoriaMetrics/lib/fs"
 	"github.com/VictoriaMetrics/VictoriaMetrics/lib/logger"
 	"github.com/VictoriaMetrics/VictoriaMetrics/lib/memory"
+	"github.com/VictoriaMetrics/VictoriaMetrics/lib/syncwg"
 	"github.com/VictoriaMetrics/VictoriaMetrics/lib/uint64set"
 )
 
@@ -1393,6 +1394,12 @@ func (pt *partition) createSnapshot(srcDir, dstDir string) error {
 }
 
 func runTransactions(txnLock *sync.RWMutex, pathPrefix1, pathPrefix2, path string) error {
+	// Wait until all the previous pending transaction deletions are finished.
+	pendingTxnDeletionsWG.Wait()
+
+	// Make sure all the current transaction deletions are finished before exiting.
+	defer pendingTxnDeletionsWG.Wait()
+
 	txnDir := path + "/txn"
 	d, err := os.Open(txnDir)
 	if err != nil {
@@ -1494,7 +1501,9 @@ func runTransaction(txnLock *sync.RWMutex, pathPrefix1, pathPrefix2, txnPath str
 	fs.MustSyncPath(pathPrefix1)
 	fs.MustSyncPath(pathPrefix2)
 
+	pendingTxnDeletionsWG.Add(1)
 	go func() {
+		defer pendingTxnDeletionsWG.Done()
 		// Remove the transaction file only after all the source paths are deleted.
 		// This is required for NFS mounts. See https://github.com/VictoriaMetrics/VictoriaMetrics/issues/61 .
 		removeWG.Wait()
@@ -1506,6 +1515,8 @@ func runTransaction(txnLock *sync.RWMutex, pathPrefix1, pathPrefix2, txnPath str
 	return nil
 }
 
+var pendingTxnDeletionsWG syncwg.WaitGroup
+
 func validatePath(pathPrefix1, pathPrefix2, path string) (string, error) {
 	var err error