diff --git a/lib/fs/fs.go b/lib/fs/fs.go
index b5c2928e8a..245bc0814e 100644
--- a/lib/fs/fs.go
+++ b/lib/fs/fs.go
@@ -211,6 +211,7 @@ func MustRemoveDirAtomic(dir string) {
 	if err := os.Rename(dir, tmpDir); err != nil {
 		logger.Panicf("FATAL: cannot move %s to %s: %s", dir, tmpDir, err)
 	}
+	MustSyncPath(dir)
 	MustRemoveAll(tmpDir)
 }
 
diff --git a/lib/storage/partition.go b/lib/storage/partition.go
index 082bc4f156..5ee2cc1e6e 100644
--- a/lib/storage/partition.go
+++ b/lib/storage/partition.go
@@ -236,8 +236,8 @@ func (pt *partition) Drop() {
 	// Wait until all the pending transaction deletions are finished before removing partition directories.
 	pendingTxnDeletionsWG.Wait()
 
-	fs.MustRemoveAll(pt.smallPartsPath)
-	fs.MustRemoveAll(pt.bigPartsPath)
+	fs.MustRemoveDirAtomic(pt.smallPartsPath)
+	fs.MustRemoveDirAtomic(pt.bigPartsPath)
 	logger.Infof("partition %q has been dropped", pt.name)
 }
 
diff --git a/lib/storage/table.go b/lib/storage/table.go
index 25ea2edb9f..cf005814bb 100644
--- a/lib/storage/table.go
+++ b/lib/storage/table.go
@@ -103,6 +103,7 @@ func openTable(path string, getDeletedMetricIDs func() *uint64set.Set, retention
 	if err := fs.MkdirAllIfNotExist(smallPartitionsPath); err != nil {
 		return nil, fmt.Errorf("cannot create directory for small partitions %q: %w", smallPartitionsPath, err)
 	}
+	fs.MustRemoveTemporaryDirs(smallPartitionsPath)
 	smallSnapshotsPath := smallPartitionsPath + "/snapshots"
 	if err := fs.MkdirAllIfNotExist(smallSnapshotsPath); err != nil {
 		return nil, fmt.Errorf("cannot create %q: %w", smallSnapshotsPath, err)
@@ -113,6 +114,7 @@ func openTable(path string, getDeletedMetricIDs func() *uint64set.Set, retention
 	if err := fs.MkdirAllIfNotExist(bigPartitionsPath); err != nil {
 		return nil, fmt.Errorf("cannot create directory for big partitions %q: %w", bigPartitionsPath, err)
 	}
+	fs.MustRemoveTemporaryDirs(bigPartitionsPath)
 	bigSnapshotsPath := bigPartitionsPath + "/snapshots"
 	if err := fs.MkdirAllIfNotExist(bigSnapshotsPath); err != nil {
 		return nil, fmt.Errorf("cannot create %q: %w", bigSnapshotsPath, err)