diff --git a/pkg/local_object_storage/metabase/delete_ec_test.go b/pkg/local_object_storage/metabase/delete_ec_test.go
index 0e627f095..99bf4aafc 100644
--- a/pkg/local_object_storage/metabase/delete_ec_test.go
+++ b/pkg/local_object_storage/metabase/delete_ec_test.go
@@ -16,6 +16,7 @@ import (
 	objectSDK "git.frostfs.info/TrueCloudLab/frostfs-sdk-go/object"
 	oid "git.frostfs.info/TrueCloudLab/frostfs-sdk-go/object/id"
 	oidtest "git.frostfs.info/TrueCloudLab/frostfs-sdk-go/object/id/test"
+	"github.com/cockroachdb/pebble"
 	"github.com/stretchr/testify/require"
 	"go.etcd.io/bbolt"
 )
@@ -107,10 +108,11 @@ func TestDeleteECObject_WithoutSplit(t *testing.T) {
 	require.True(t, slices.Contains(garbageAddresses, ecParentAddress))
 	require.True(t, slices.Contains(garbageAddresses, ecChunkAddress))
 
-	var deletePrm DeletePrm
-	deletePrm.SetAddresses(garbageAddresses...)
-	_, err = db.Delete(context.Background(), deletePrm)
-	require.NoError(t, err)
+	for _, a := range garbageAddresses {
+		deletePrm := DeletePrm{Address: a}
+		_, err = db.Delete(context.Background(), deletePrm)
+		require.NoError(t, err)
+	}
 
 	garbageAddresses = nil
 	itPrm.SetHandler(func(g GarbageObject) error {
@@ -153,9 +155,11 @@ func TestDeleteECObject_WithoutSplit(t *testing.T) {
 	require.Equal(t, 1, len(garbageAddresses))
 	require.Equal(t, tombstoneID, garbageAddresses[0].Object())
 
-	deletePrm.SetAddresses(garbageAddresses...)
-	_, err = db.Delete(context.Background(), deletePrm)
-	require.NoError(t, err)
+	for _, a := range garbageAddresses {
+		deletePrm := DeletePrm{Address: a}
+		_, err = db.Delete(context.Background(), deletePrm)
+		require.NoError(t, err)
+	}
 
 	// no more objects should left as garbage
 
@@ -165,7 +169,7 @@ func TestDeleteECObject_WithoutSplit(t *testing.T) {
 	})
 	require.NoError(t, db.IterateOverGarbage(context.Background(), itPrm))
 
-	require.NoError(t, db.boltDB.View(testVerifyNoObjectDataLeft))
+	require.NoError(t, testVerifyNoObjectDataLeft(db.database.NewSnapshot()))
 
 	require.NoError(t, testCountersAreZero(db, cnr))
 }
@@ -351,10 +355,11 @@ func testDeleteECObjectWithSplit(t *testing.T, chunksCount int, withLinking bool
 		require.True(t, slices.Contains(garbageAddresses, ecChunkAddress))
 	}
 
-	var deletePrm DeletePrm
-	deletePrm.SetAddresses(garbageAddresses...)
-	_, err = db.Delete(context.Background(), deletePrm)
-	require.NoError(t, err)
+	for _, a := range garbageAddresses {
+		deletePrm := DeletePrm{Address: a}
+		_, err = db.Delete(context.Background(), deletePrm)
+		require.NoError(t, err)
+	}
 
 	var garbageStub []oid.Address
 	itPrm.SetHandler(func(g GarbageObject) error {
@@ -397,9 +402,11 @@ func testDeleteECObjectWithSplit(t *testing.T, chunksCount int, withLinking bool
 	require.Equal(t, 1, len(garbageAddresses))
 	require.Equal(t, tombstoneID, garbageAddresses[0].Object())
 
-	deletePrm.SetAddresses(garbageAddresses...)
-	_, err = db.Delete(context.Background(), deletePrm)
-	require.NoError(t, err)
+	for _, a := range garbageAddresses {
+		deletePrm := DeletePrm{Address: a}
+		_, err = db.Delete(context.Background(), deletePrm)
+		require.NoError(t, err)
+	}
 
 	// no more objects should left as garbage
 
@@ -409,20 +416,32 @@ func testDeleteECObjectWithSplit(t *testing.T, chunksCount int, withLinking bool
 	})
 	require.NoError(t, db.IterateOverGarbage(context.Background(), itPrm))
 
-	require.NoError(t, db.boltDB.View(testVerifyNoObjectDataLeft))
+	require.NoError(t, testVerifyNoObjectDataLeft(db.database.NewSnapshot()))
 
 	require.NoError(t, testCountersAreZero(db, cnr))
 }
 
-func testVerifyNoObjectDataLeft(tx *bbolt.Tx) error {
-	return tx.ForEach(func(name []byte, b *bbolt.Bucket) error {
-		if bytes.Equal(name, shardInfoBucket) ||
-			bytes.Equal(name, containerCounterBucketName) ||
-			bytes.Equal(name, containerVolumeBucketName) {
-			return nil
+func testVerifyNoObjectDataLeft(s *pebble.Snapshot) error {
+	defer s.Close()
+	it, err := s.NewIter(nil)
+	if err != nil {
+		return err
+	}
+	for v := it.First(); v; v = it.Next() {
+		if bytes.Equal(it.Key(), shardInfoKey(versionKey)) ||
+			bytes.HasPrefix(it.Key(), []byte{containerCountersPrefix}) ||
+			bytes.HasPrefix(it.Key(), []byte{containerSizePrefix}) {
+			continue
 		}
-		return testBucketEmpty(name, b)
-	})
+
+		err := it.Close()
+		if err != nil {
+			return err
+		}
+		return fmt.Errorf("database is not empty, key %s found", string(it.Key()))
+	}
+
+	return it.Close()
 }
 
 func testBucketEmpty(name []byte, b *bbolt.Bucket) error {
@@ -448,7 +467,7 @@ func testCountersAreZero(db *DB, cnr cid.ID) error {
 	if !c.IsZero() {
 		return fmt.Errorf("container %s has non zero counters", cnr.EncodeToString())
 	}
-	s, err := db.ContainerSize(cnr)
+	s, err := db.ContainerSize(context.Background(), cnr)
 	if err != nil {
 		return err
 	}
diff --git a/pkg/local_object_storage/metabase/inhume.go b/pkg/local_object_storage/metabase/inhume.go
index 1c66758c9..fc344d726 100644
--- a/pkg/local_object_storage/metabase/inhume.go
+++ b/pkg/local_object_storage/metabase/inhume.go
@@ -227,7 +227,7 @@ func (db *DB) inhumeTx(ctx context.Context, b *pebble.Batch, epoch uint64, prm I
 				return err
 			}
 		} else if errors.As(err, &ecErr) {
-			err = db.inhumeECInfo(ctx, b, epoch, keyer, value, res, ecErr.ECInfo(), cnr)
+			err = db.inhumeECInfo(ctx, b, epoch, prm.tomb, keyer, value, res, ecErr.ECInfo(), cnr)
 			if err != nil {
 				return err
 			}
@@ -272,7 +272,7 @@ func (db *DB) inhumeTx(ctx context.Context, b *pebble.Batch, epoch uint64, prm I
 	return db.applyInhumeResToCounters(b, res)
 }
 
-func (db *DB) inhumeECInfo(ctx context.Context, b *pebble.Batch, epoch uint64,
+func (db *DB) inhumeECInfo(ctx context.Context, b *pebble.Batch, epoch uint64, tomb *oid.Address,
 	keyer func(addr oid.Address) []byte, value []byte,
 	res *InhumeRes, ecInfo *objectSDK.ECInfo, cnr cid.ID,
 ) error {
@@ -293,6 +293,12 @@ func (db *DB) inhumeECInfo(ctx context.Context, b *pebble.Batch, epoch uint64,
 		if err != nil {
 			return err
 		}
+		if tomb != nil {
+			_, err = markAsGC(b, chunkAddr)
+			if err != nil {
+				return err
+			}
+		}
 		key := keyer(chunkAddr)
 		err = b.Set(key, value, pebble.Sync)
 		if err != nil {