diff --git a/pkg/local_object_storage/metabase/upgrade.go b/pkg/local_object_storage/metabase/upgrade.go
index a997b90a0..1f2c7956b 100644
--- a/pkg/local_object_storage/metabase/upgrade.go
+++ b/pkg/local_object_storage/metabase/upgrade.go
@@ -360,26 +360,40 @@ func dropUserAttributes(ctx context.Context, db *bbolt.DB, cs container.InfoProv
 			return nil
 		}
 		last = keys[len(keys)-1]
-		keysToDrop, err := selectUserAttributeKeysToDrop(keys, cs)
+		cnt, err := dropNonIndexedUserAttributeBuckets(db, cs, keys)
 		if err != nil {
+			log("deleting user attribute buckets completed with an error:", err)
 			return err
 		}
-		if err := db.Batch(func(tx *bbolt.Tx) error {
-			for _, k := range keysToDrop {
-				if err := tx.DeleteBucket(k); err != nil {
-					return err
-				}
-			}
-			return nil
-		}); err != nil {
-			log("deleting buckets completed with an error:", err)
+		count += cnt
+		cnt, err = dropEmptyUserAttributeBuckets(ctx, db, keys)
+		if err != nil {
+			log("deleting user attribute buckets completed with an error:", err)
 			return err
 		}
-		count += uint64(len(keysToDrop))
-		log("deleted", count, "buckets")
+		count += cnt
+		log("deleted", count, "user attribute buckets")
 	}
 }
 
+func dropNonIndexedUserAttributeBuckets(db *bbolt.DB, cs container.InfoProvider, keys [][]byte) (uint64, error) {
+	keysToDrop, err := selectUserAttributeKeysToDrop(keys, cs)
+	if err != nil {
+		return 0, fmt.Errorf("select non indexed user attributes: %w", err)
+	}
+	if err := db.Batch(func(tx *bbolt.Tx) error {
+		for _, k := range keysToDrop {
+			if err := tx.DeleteBucket(k); err != nil {
+				return err
+			}
+		}
+		return nil
+	}); err != nil {
+		return 0, fmt.Errorf("drop non indexed user attributes: %w", err)
+	}
+	return uint64(len(keysToDrop)), nil
+}
+
 func selectUserAttributeKeysToDrop(keys [][]byte, cs container.InfoProvider) ([][]byte, error) {
 	var keysToDrop [][]byte
 	for _, key := range keys {
@@ -406,6 +420,134 @@ func selectUserAttributeKeysToDrop(keys [][]byte, cs container.InfoProvider) ([]
 	return keysToDrop, nil
 }
 
+func dropEmptyUserAttributeBuckets(ctx context.Context, db *bbolt.DB, keys [][]byte) (uint64, error) {
+	var dropBuckets [][]byte
+	for _, key := range keys {
+		select {
+		case <-ctx.Done():
+			return 0, ctx.Err()
+		default:
+		}
+
+		if err := dropEmptyNestedBuckets(ctx, db, key); err != nil {
+			return 0, err
+		}
+
+		empty, exists, err := bucketIsEmpty(db, key)
+		if err != nil {
+			return 0, err
+		}
+		if empty && exists {
+			dropBuckets = append(dropBuckets, key)
+		}
+	}
+	if len(dropBuckets) == 0 {
+		return 0, nil
+	}
+	if err := db.Batch(func(tx *bbolt.Tx) error {
+		for _, key := range dropBuckets {
+			if err := tx.DeleteBucket(key); err != nil {
+				return err
+			}
+		}
+		return nil
+	}); err != nil {
+		return 0, fmt.Errorf("drop empty user attributes buckets: %w", err)
+	}
+	return uint64(len(dropBuckets)), nil
+}
+
+func bucketIsEmpty(db *bbolt.DB, bucketKey []byte) (bool, bool, error) {
+	var empty bool
+	var exists bool
+	if err := db.View(func(tx *bbolt.Tx) error {
+		b := tx.Bucket(bucketKey)
+		if b == nil {
+			return nil
+		}
+		exists = true
+		empty = !hasAnyItem(b)
+		return nil
+	}); err != nil {
+		return false, false, fmt.Errorf("bucket empty check: %w", err)
+	}
+	return empty, exists, nil
+}
+
+func dropEmptyNestedBuckets(ctx context.Context, db *bbolt.DB, rootBucketKey []byte) error {
+	var last []byte
+	for {
+		select {
+		case <-ctx.Done():
+			return ctx.Err()
+		default:
+		}
+
+		var dropBuckets [][]byte
+		var err error
+		dropBuckets, last, err = selectEmptyNestedBuckets(ctx, db, rootBucketKey, last)
+		if err != nil {
+			return fmt.Errorf("select empty nested buckets: %w", err)
+		}
+		if len(dropBuckets) == 0 {
+			return nil
+		}
+
+		if err := db.Batch(func(tx *bbolt.Tx) error {
+			rootBucket := tx.Bucket(rootBucketKey)
+			if rootBucket == nil {
+				return nil
+			}
+			for _, sb := range dropBuckets {
+				if err := rootBucket.DeleteBucket(sb); err != nil {
+					return err
+				}
+			}
+			return nil
+		}); err != nil {
+			return fmt.Errorf("drop empty nested buckets: %w", err)
+		}
+	}
+}
+
+func selectEmptyNestedBuckets(ctx context.Context, db *bbolt.DB, rootBucketKey, last []byte) ([][]byte, []byte, error) {
+	const batchSize = 1000
+	var result [][]byte
+	if err := db.View(func(tx *bbolt.Tx) error {
+		rootBucket := tx.Bucket(rootBucketKey)
+		if rootBucket == nil {
+			return nil
+		}
+		c := rootBucket.Cursor()
+		for k, v := c.Seek(last); k != nil && len(result) < batchSize; k, v = c.Next() {
+			select {
+			case <-ctx.Done():
+				return ctx.Err()
+			default:
+			}
+
+			if bytes.Equal(last, k) {
+				continue
+			}
+			last = bytes.Clone(k)
+			if v != nil { // record
+				continue
+			}
+			nestedBucket := rootBucket.Bucket(k)
+			if nestedBucket == nil {
+				continue
+			}
+			if !hasAnyItem(nestedBucket) {
+				result = append(result, bytes.Clone(k))
+			}
+		}
+		return nil
+	}); err != nil {
+		return nil, nil, err
+	}
+	return result, last, nil
+}
+
 func dropOwnerIDIndex(ctx context.Context, db *bbolt.DB, log func(a ...any)) error {
 	return dropBucketsByPrefix(ctx, db, []byte{ownerPrefix}, func(a ...any) {
 		log(append([]any{"owner ID index:"}, a...)...)