diff --git a/pkg/local_object_storage/metabase/version.go b/pkg/local_object_storage/metabase/version.go
index 5748b64ee..c65902d71 100644
--- a/pkg/local_object_storage/metabase/version.go
+++ b/pkg/local_object_storage/metabase/version.go
@@ -5,7 +5,7 @@ import (
 	"fmt"
 
 	"git.frostfs.info/TrueCloudLab/frostfs-node/pkg/local_object_storage/util/logicerr"
-	"go.etcd.io/bbolt"
+	"github.com/cockroachdb/pebble"
 )
 
 // version contains current metabase version.
@@ -18,25 +18,25 @@ var versionKey = []byte("version")
 // the current code version.
 var ErrOutdatedVersion = logicerr.New("invalid version, resynchronization is required")
 
-func checkVersion(tx *bbolt.Tx, initialized bool) error {
+func checkVersion(b *pebble.Batch, initialized bool) error {
 	var knownVersion bool
 
-	b := tx.Bucket(shardInfoBucket)
-	if b != nil {
-		data := b.Get(versionKey)
-		if len(data) == 8 {
-			knownVersion = true
+	data, err := valueSafe(b, shardInfoKey(versionKey))
+	if err != nil {
+		return err
+	}
+	if len(data) == 8 {
+		knownVersion = true
 
-			stored := binary.LittleEndian.Uint64(data)
-			if stored != version {
-				return fmt.Errorf("%w: expected=%d, stored=%d", ErrOutdatedVersion, version, stored)
-			}
+		stored := binary.LittleEndian.Uint64(data)
+		if stored != version {
+			return fmt.Errorf("%w: expected=%d, stored=%d", ErrOutdatedVersion, version, stored)
 		}
 	}
 
 	if !initialized {
 		// new database, write version
-		return updateVersion(tx, version)
+		return updateVersion(b, version)
 	} else if !knownVersion {
 		// db is initialized but no version
 		// has been found; that could happen
@@ -49,13 +49,8 @@ func checkVersion(tx *bbolt.Tx, initialized bool) error {
 	return nil
 }
 
-func updateVersion(tx *bbolt.Tx, version uint64) error {
+func updateVersion(b *pebble.Batch, version uint64) error {
 	data := make([]byte, 8)
 	binary.LittleEndian.PutUint64(data, version)
-
-	b, err := tx.CreateBucketIfNotExists(shardInfoBucket)
-	if err != nil {
-		return fmt.Errorf("can't create auxiliary bucket: %w", err)
-	}
-	return b.Put(versionKey, data)
+	return b.Set(shardInfoKey(versionKey), data, pebble.Sync)
 }