diff --git a/pkg/local_object_storage/metabase/db_test.go b/pkg/local_object_storage/metabase/db_test.go
index eb31866303..8939670c04 100644
--- a/pkg/local_object_storage/metabase/db_test.go
+++ b/pkg/local_object_storage/metabase/db_test.go
@@ -26,16 +26,32 @@ func testSelect(t *testing.T, db *DB, fs objectSDK.SearchFilters, exp ...*object
 	}
 }
 
+func testCID() *container.ID {
+	cs := [sha256.Size]byte{}
+	rand.Read(cs[:])
+
+	id := container.NewID()
+	id.SetSHA256(cs)
+
+	return id
+}
+
+func testOID() *objectSDK.ID {
+	cs := [sha256.Size]byte{}
+	rand.Read(cs[:])
+
+	id := objectSDK.NewID()
+	id.SetSHA256(cs)
+
+	return id
+}
+
 func TestDB(t *testing.T) {
 	version := pkg.NewVersion()
 	version.SetMajor(2)
 	version.SetMinor(1)
 
-	cs := [sha256.Size]byte{}
-	rand.Read(cs[:])
-
-	cid := container.NewID()
-	cid.SetSHA256(cs)
+	cid := testCID()
 
 	w, err := owner.NEO3WalletFromPublicKey(&test.DecodeKey(-1).PublicKey)
 	require.NoError(t, err)
@@ -43,9 +59,7 @@ func TestDB(t *testing.T) {
 	ownerID := owner.NewID()
 	ownerID.SetNeo3Wallet(w)
 
-	rand.Read(cs[:])
-	oid := objectSDK.NewID()
-	oid.SetSHA256(cs)
+	oid := testOID()
 
 	obj := object.NewRaw()
 	obj.SetID(oid)
@@ -100,3 +114,42 @@ func TestDB(t *testing.T) {
 	fs.AddFilter(k, v+"1", objectSDK.MatchStringEqual)
 	testSelect(t, db, fs)
 }
+
+func TestDB_Delete(t *testing.T) {
+	path := "test.db"
+
+	bdb, err := bbolt.Open(path, 0600, nil)
+	require.NoError(t, err)
+
+	defer func() {
+		bdb.Close()
+		os.Remove(path)
+	}()
+
+	db := NewDB(bdb)
+
+	obj := object.NewRaw()
+	obj.SetContainerID(testCID())
+	obj.SetID(testOID())
+
+	o := obj.Object()
+
+	require.NoError(t, db.Put(o))
+
+	addr := o.Address()
+
+	_, err = db.Get(addr)
+	require.NoError(t, err)
+
+	fs := objectSDK.SearchFilters{}
+	fs.AddObjectContainerIDFilter(objectSDK.MatchStringEqual, o.GetContainerID())
+
+	testSelect(t, db, fs, o.Address())
+
+	require.NoError(t, db.Delete(addr))
+
+	_, err = db.Get(addr)
+	require.Error(t, err)
+
+	testSelect(t, db, fs)
+}
diff --git a/pkg/local_object_storage/metabase/delete.go b/pkg/local_object_storage/metabase/delete.go
new file mode 100644
index 0000000000..0690b7060b
--- /dev/null
+++ b/pkg/local_object_storage/metabase/delete.go
@@ -0,0 +1,31 @@
+package meta
+
+import (
+	"github.com/nspcc-dev/neofs-api-go/pkg/object"
+	"github.com/pkg/errors"
+	"go.etcd.io/bbolt"
+)
+
+var tombstoneBucket = []byte("tombstones")
+
+// Delete marks object as deleted.
+func (db *DB) Delete(addr *object.Address) error {
+	return db.boltDB.Update(func(tx *bbolt.Tx) error {
+		bucket, err := tx.CreateBucketIfNotExists(tombstoneBucket)
+		if err != nil {
+			return errors.Wrapf(err, "(%T) could not create tombstone bucket", db)
+		}
+
+		if err := bucket.Put(addressKey(addr), nil); err != nil {
+			return errors.Wrapf(err, "(%T) could not put to tombstone bucket", db)
+		}
+
+		return nil
+	})
+}
+
+func objectRemoved(tx *bbolt.Tx, addr []byte) bool {
+	tombstoneBucket := tx.Bucket(tombstoneBucket)
+
+	return tombstoneBucket != nil && tombstoneBucket.Get(addr) != nil
+}
diff --git a/pkg/local_object_storage/metabase/get.go b/pkg/local_object_storage/metabase/get.go
index 445c553b51..498cc2a06d 100644
--- a/pkg/local_object_storage/metabase/get.go
+++ b/pkg/local_object_storage/metabase/get.go
@@ -15,12 +15,19 @@ func (db *DB) Get(addr *objectSDK.Address) (*object.Object, error) {
 	var obj *object.Object
 
 	if err := db.boltDB.View(func(tx *bbolt.Tx) error {
+		addrKey := addressKey(addr)
+
+		// check if object marked as deleted
+		if objectRemoved(tx, addrKey) {
+			return errNotFound
+		}
+
 		primaryBucket := tx.Bucket(primaryBucket)
 		if primaryBucket == nil {
 			return errNotFound
 		}
 
-		data := primaryBucket.Get(addressKey(addr))
+		data := primaryBucket.Get(addrKey)
 		if data == nil {
 			return errNotFound
 		}
diff --git a/pkg/local_object_storage/metabase/select.go b/pkg/local_object_storage/metabase/select.go
index 227f483c46..b363671ed1 100644
--- a/pkg/local_object_storage/metabase/select.go
+++ b/pkg/local_object_storage/metabase/select.go
@@ -67,6 +67,11 @@ func (db *DB) Select(fs object.SearchFilters) ([]*object.Address, error) {
 				return nil
 			}
 
+			// check if object marked as deleted
+			if objectRemoved(tx, k) {
+				return nil
+			}
+
 			addr := object.NewAddress()
 			if err := addr.Parse(string(k)); err != nil {
 				// TODO: storage was broken, so we need to handle it