diff --git a/pkg/local_object_storage/metabase/containers.go b/pkg/local_object_storage/metabase/containers.go
index 5fae1f72e..c8a1318bc 100644
--- a/pkg/local_object_storage/metabase/containers.go
+++ b/pkg/local_object_storage/metabase/containers.go
@@ -1,14 +1,23 @@
 package meta
 
 import (
+	"bytes"
 	"context"
 	"encoding/binary"
+	"fmt"
 	"time"
 
 	"git.frostfs.info/TrueCloudLab/frostfs-node/pkg/local_object_storage/internal/metaerr"
 	"git.frostfs.info/TrueCloudLab/frostfs-observability/tracing"
 	cid "git.frostfs.info/TrueCloudLab/frostfs-sdk-go/container/id"
-	"go.etcd.io/bbolt"
+	"github.com/cockroachdb/pebble"
+	"go.opentelemetry.io/otel/attribute"
+	"go.opentelemetry.io/otel/trace"
+)
+
+const (
+	containerSizeKeySize    = 1 + cidSize + 2
+	containerSizePrefixSize = 1 + cidSize
 )
 
 func (db *DB) Containers(ctx context.Context) (list []cid.ID, err error) {
@@ -30,8 +39,8 @@ func (db *DB) Containers(ctx context.Context) (list []cid.ID, err error) {
 		return nil, ErrDegradedMode
 	}
 
-	err = db.database.View(func(tx *bbolt.Tx) error {
-		list, err = db.containers(tx)
+	err = db.snapshot(func(s *pebble.Snapshot) error {
+		list, err = containers(ctx, s)
 
 		return err
 	})
@@ -39,50 +48,30 @@ func (db *DB) Containers(ctx context.Context) (list []cid.ID, err error) {
 	return list, metaerr.Wrap(err)
 }
 
-func (db *DB) containers(tx *bbolt.Tx) ([]cid.ID, error) {
+func containers(ctx context.Context, r pebble.Reader) ([]cid.ID, error) {
 	result := make([]cid.ID, 0)
 	unique := make(map[string]struct{})
 	var cnr cid.ID
 
-	err := tx.ForEach(func(name []byte, _ *bbolt.Bucket) error {
-		if parseContainerID(&cnr, name, unique) {
-			result = append(result, cnr)
-			unique[string(name[1:bucketKeySize])] = struct{}{}
-		}
-
-		return nil
+	it, err := r.NewIter(&pebble.IterOptions{
+		OnlyReadGuaranteedDurable: true,
 	})
-
-	return result, err
-}
-
-func (db *DB) ContainerSize(id cid.ID) (size uint64, err error) {
-	db.modeMtx.RLock()
-	defer db.modeMtx.RUnlock()
-
-	if db.mode.NoMetabase() {
-		return 0, ErrDegradedMode
+	if err != nil {
+		return nil, err
 	}
 
-	err = db.database.View(func(tx *bbolt.Tx) error {
-		size, err = db.containerSize(tx, id)
+	for v := it.First(); v; v = it.Next() {
+		if parseContainerIDWithIgnore(&cnr, it.Key(), unique) {
+			result = append(result, cnr)
+			unique[string(it.Key()[1:containerSizePrefixSize])] = struct{}{}
+		}
+	}
 
-		return err
-	})
-
-	return size, metaerr.Wrap(err)
+	return result, nil
 }
 
-func (db *DB) containerSize(tx *bbolt.Tx, id cid.ID) (uint64, error) {
-	containerVolume := tx.Bucket(containerVolumeBucketName)
-	key := make([]byte, cidSize)
-	id.Encode(key)
-
-	return parseContainerSize(containerVolume.Get(key)), nil
-}
-
-func parseContainerID(dst *cid.ID, name []byte, ignore map[string]struct{}) bool {
-	if len(name) != bucketKeySize {
+func parseContainerIDWithIgnore(dst *cid.ID, name []byte, ignore map[string]struct{}) bool {
+	if len(name) < bucketKeySize {
 		return false
 	}
 	if _, ok := ignore[string(name[1:bucketKeySize])]; ok {
@@ -91,31 +80,194 @@ func parseContainerID(dst *cid.ID, name []byte, ignore map[string]struct{}) bool
 	return dst.Decode(name[1:bucketKeySize]) == nil
 }
 
-func parseContainerSize(v []byte) uint64 {
+func (db *DB) ContainerSize(ctx context.Context, id cid.ID) (size uint64, err error) {
+	db.modeMtx.RLock()
+	defer db.modeMtx.RUnlock()
+
+	if db.mode.NoMetabase() {
+		return 0, ErrDegradedMode
+	}
+
+	result, err := db.containerSizesInternal(ctx, &id)
+	if err != nil {
+		return 0, metaerr.Wrap(err)
+	}
+	return result[id], nil
+}
+
+func (db *DB) ContainerSizes(ctx context.Context) (map[cid.ID]uint64, error) {
+	db.modeMtx.RLock()
+	defer db.modeMtx.RUnlock()
+
+	if db.mode.NoMetabase() {
+		return nil, ErrDegradedMode
+	}
+
+	return db.containerSizesInternal(ctx, nil)
+}
+
+// ZeroSizeContainers returns containers with size = 0.
+func (db *DB) ZeroSizeContainers(ctx context.Context) ([]cid.ID, error) {
+	var (
+		startedAt = time.Now()
+		success   = false
+	)
+	defer func() {
+		db.metrics.AddMethodDuration("ZeroSizeContainers", time.Since(startedAt), success)
+	}()
+
+	ctx, span := tracing.StartSpanFromContext(ctx, "metabase.ZeroSizeContainers")
+	defer span.End()
+
+	db.modeMtx.RLock()
+	defer db.modeMtx.RUnlock()
+
+	sizes, err := db.containerSizesInternal(ctx, nil)
+	if err != nil {
+		return nil, err
+	}
+	var result []cid.ID
+	for id, size := range sizes {
+		if size == 0 {
+			result = append(result, id)
+		}
+	}
+	return result, nil
+}
+
+func (db *DB) DeleteContainerSize(ctx context.Context, id cid.ID) error {
+	var (
+		startedAt = time.Now()
+		success   = false
+	)
+	defer func() {
+		db.metrics.AddMethodDuration("DeleteContainerSize", time.Since(startedAt), success)
+	}()
+
+	_, span := tracing.StartSpanFromContext(ctx, "metabase.DeleteContainerSize",
+		trace.WithAttributes(
+			attribute.Stringer("container_id", id),
+		))
+	defer span.End()
+
+	db.modeMtx.RLock()
+	defer db.modeMtx.RUnlock()
+
+	if db.mode.NoMetabase() {
+		return ErrDegradedMode
+	}
+
+	if db.mode.ReadOnly() {
+		return ErrReadOnlyMode
+	}
+
+	return metaerr.Wrap(db.batch(
+		func(b *pebble.Batch) error {
+			return deleteByPrefix(ctx, b, containerSizeKeyPrefix(id))
+		}))
+}
+
+func (db *DB) containerSizesInternal(ctx context.Context, id *cid.ID) (map[cid.ID]uint64, error) {
+	prefix := []byte{containerSizePrefix}
+	if id != nil {
+		prefix = containerSizeKeyPrefix(*id)
+	}
+	result := make(map[cid.ID]int64)
+	err := db.snapshot(func(s *pebble.Snapshot) error {
+		it, err := s.NewIter(&pebble.IterOptions{
+			LowerBound:                prefix,
+			OnlyReadGuaranteedDurable: true,
+		})
+		if err != nil {
+			return err
+		}
+
+		for v := it.First(); v && bytes.HasPrefix(it.Key(), prefix); v = it.Next() {
+			select {
+			case <-ctx.Done():
+				return ctx.Err()
+			default:
+			}
+
+			key := it.Key()
+			var cnr cid.ID
+			if err := cnr.Decode(key[1:containerSizePrefixSize]); err != nil {
+				return fmt.Errorf("invalid container size key: %w", err)
+			}
+
+			value, ok := parseSize(it.Value())
+			if !ok {
+				return fmt.Errorf("invalid container size value for container %s", cnr)
+			}
+			result[cnr] += value
+		}
+		return nil
+	})
+	if err != nil {
+		return nil, metaerr.Wrap(err)
+	}
+
+	return normilizeContainerSizes(result)
+}
+
+func normilizeContainerSizes(sizes map[cid.ID]int64) (map[cid.ID]uint64, error) {
+	result := make(map[cid.ID]uint64, len(sizes))
+	for k, v := range sizes {
+		if v < 0 {
+			return nil, fmt.Errorf("invalid cumulative size for container %s", k)
+		}
+		result[k] = uint64(v)
+	}
+	return result, nil
+}
+
+func changeContainerSize(b *pebble.Batch, id cid.ID, delta int64, bucketID uint16) error {
+	key := containerSizeKey(id, bucketID)
+
+	v, err := valueSafe(b, key)
+	if err != nil {
+		return err
+	}
+
+	size, ok := parseSize(v)
+	if !ok {
+		return fmt.Errorf("invalid container size value for container %s", id)
+	}
+
+	size += delta
+	value := marshalSize(size)
+	return b.Set(key, value, pebble.Sync)
+}
+
+// containerSizeKeyPrefix returns containerSizePrefix_CID key prefix.
+func containerSizeKeyPrefix(cnr cid.ID) []byte {
+	result := make([]byte, containerSizePrefixSize)
+	result[0] = containerSizePrefix
+	cnr.Encode(result[1:])
+	return result
+}
+
+// containerSizeKey returns containerVolumePrefix_CID_bucketID key.
+func containerSizeKey(cnr cid.ID, bucketID uint16) []byte {
+	result := make([]byte, containerSizeKeySize)
+	result[0] = containerSizePrefix
+	cnr.Encode(result[1:])
+	binary.LittleEndian.PutUint16(result[containerSizePrefixSize:], bucketID)
+	return result
+}
+
+func parseSize(v []byte) (int64, bool) {
 	if len(v) == 0 {
-		return 0
+		return 0, true
 	}
-
-	return binary.LittleEndian.Uint64(v)
+	if len(v) != 8 {
+		return 0, false
+	}
+	return int64(binary.LittleEndian.Uint64(v)), true
 }
 
-func changeContainerSize(tx *bbolt.Tx, id cid.ID, delta uint64, increase bool) error {
-	containerVolume := tx.Bucket(containerVolumeBucketName)
-	key := make([]byte, cidSize)
-	id.Encode(key)
-
-	size := parseContainerSize(containerVolume.Get(key))
-
-	if increase {
-		size += delta
-	} else if size > delta {
-		size -= delta
-	} else {
-		size = 0
-	}
-
-	buf := make([]byte, 8) // consider using sync.Pool to decrease allocations
-	binary.LittleEndian.PutUint64(buf, size)
-
-	return containerVolume.Put(key, buf)
+func marshalSize(v int64) []byte {
+	buf := make([]byte, 8)
+	binary.LittleEndian.PutUint64(buf, uint64(v))
+	return buf
 }
diff --git a/pkg/local_object_storage/metabase/pebble.go b/pkg/local_object_storage/metabase/pebble.go
index 9921ce119..3f94289c1 100644
--- a/pkg/local_object_storage/metabase/pebble.go
+++ b/pkg/local_object_storage/metabase/pebble.go
@@ -67,3 +67,26 @@ func selectByPrefixBatch(ctx context.Context, r pebble.Reader, prefix []byte, ba
 	}
 	return result, it.Close()
 }
+
+func deleteByPrefix(ctx context.Context, b *pebble.Batch, prefix []byte) error {
+	for {
+		batch, err := selectByPrefixBatch(ctx, b, prefix, batchSize)
+		if err != nil {
+			return err
+		}
+		for _, key := range batch {
+			select {
+			case <-ctx.Done():
+				return ctx.Err()
+			default:
+			}
+
+			if err := b.Delete(key, pebble.Sync); err != nil {
+				return err
+			}
+		}
+		if len(batch) < batchSize {
+			return nil
+		}
+	}
+}