diff --git a/pkg/local_object_storage/metabase/v2/cleanup.go b/pkg/local_object_storage/metabase/v2/cleanup.go
new file mode 100644
index 000000000..9272e90ad
--- /dev/null
+++ b/pkg/local_object_storage/metabase/v2/cleanup.go
@@ -0,0 +1,85 @@
+package meta
+
+import (
+	"strings"
+
+	"go.etcd.io/bbolt"
+)
+
+func (db *DB) CleanUp() error {
+	return db.boltDB.Update(func(tx *bbolt.Tx) error {
+		return tx.ForEach(func(name []byte, b *bbolt.Bucket) error {
+			switch {
+			case isFKBTBucket(name):
+				cleanUpFKBT(tx, name, b)
+			case isListBucket(name):
+				cleanUpListBucket(tx, name, b)
+			default:
+				cleanUpUniqueBucket(tx, name, b)
+			}
+
+			return nil
+		})
+	})
+}
+
+func isFKBTBucket(name []byte) bool {
+	bucketName := string(name)
+
+	switch {
+	case
+		strings.Contains(bucketName, userAttributePostfix),
+		strings.Contains(bucketName, ownerPostfix):
+		return true
+	default:
+		return false
+	}
+}
+
+func isListBucket(name []byte) bool {
+	bucketName := string(name)
+
+	switch {
+	case
+		strings.Contains(bucketName, payloadHashPostfix),
+		strings.Contains(bucketName, parentPostfix):
+		return true
+	default:
+		return false
+	}
+}
+
+func cleanUpUniqueBucket(tx *bbolt.Tx, name []byte, b *bbolt.Bucket) {
+	if b.Stats().KeyN == 0 {
+		_ = tx.DeleteBucket(name) // ignore error, best effort there
+	}
+}
+
+func cleanUpFKBT(tx *bbolt.Tx, name []byte, b *bbolt.Bucket) {
+	removedBuckets := 0
+	remainingBuckets := b.Stats().BucketN - 1
+
+	_ = b.ForEach(func(k, _ []byte) error {
+		fkbtRoot := b.Bucket(k)
+		if fkbtRoot == nil {
+			return nil
+		}
+
+		if fkbtRoot.Stats().KeyN == 0 {
+			err := b.DeleteBucket(k)
+			if err == nil {
+				removedBuckets++
+			}
+		}
+
+		return nil
+	})
+
+	if remainingBuckets == removedBuckets {
+		_ = tx.DeleteBucket(name) // ignore error, best effort there
+	}
+}
+
+func cleanUpListBucket(tx *bbolt.Tx, name []byte, b *bbolt.Bucket) {
+	cleanUpUniqueBucket(tx, name, b)
+}