diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0ea4e78114..57bc06aa6c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,7 @@ Changelog for NeoFS Node
 ### Fixed
 - Zero range denial by `neofs-cli object range|hash` commands (#3182)
 - Not all the components needed for write-cache migration were initialized (#3186)
+- Homomorphic hash indexes with empty values in meta bucket (#3187)
 
 ### Changed
 
diff --git a/pkg/local_object_storage/metabase/metadata.go b/pkg/local_object_storage/metabase/metadata.go
index 857248302e..9309eb0d4c 100644
--- a/pkg/local_object_storage/metabase/metadata.go
+++ b/pkg/local_object_storage/metabase/metadata.go
@@ -111,8 +111,10 @@ func putMetadata(tx *bbolt.Tx, cnr cid.ID, id oid.ID, ver version.Version, owner
 	if err = putPlainAttribute(metaBkt, &keyBuf, id, object.FilterPayloadChecksum, string(pldHash)); err != nil {
 		return err
 	}
-	if err = putPlainAttribute(metaBkt, &keyBuf, id, object.FilterPayloadHomomorphicHash, string(pldHmmHash)); err != nil {
-		return err
+	if len(pldHmmHash) > 0 {
+		if err = putPlainAttribute(metaBkt, &keyBuf, id, object.FilterPayloadHomomorphicHash, string(pldHmmHash)); err != nil {
+			return err
+		}
 	}
 	if len(splitID) > 0 {
 		if err = putPlainAttribute(metaBkt, &keyBuf, id, object.FilterSplitID, string(splitID)); err != nil {
diff --git a/pkg/local_object_storage/metabase/metadata_test.go b/pkg/local_object_storage/metabase/metadata_test.go
index 73058dde44..44679265fd 100644
--- a/pkg/local_object_storage/metabase/metadata_test.go
+++ b/pkg/local_object_storage/metabase/metadata_test.go
@@ -193,6 +193,23 @@ func TestPutMetadata(t *testing.T) {
 		return nil
 	})
 	require.NoError(t, err)
+
+	t.Run("no homomorphic checksum", func(t *testing.T) {
+		cnr := cidtest.OtherID(cnr)
+		var obj object.Object
+		obj.SetContainerID(cnr)
+		obj.SetID(id)
+		obj.SetPayloadChecksum(pldHash) // Put requires
+
+		require.NoError(t, db.Put(&obj, nil, nil))
+
+		require.NoError(t, db.boltDB.View(func(tx *bbolt.Tx) error {
+			mb := tx.Bucket(append([]byte{0xFF}, cnr[:]...))
+			require.NotNil(t, mb, "missing container's meta bucket")
+			assertAttrPresence(t, mb, id, "$Object:homomorphicHash", "", false)
+			return nil
+		}))
+	})
 }
 
 func TestApplyFilter(t *testing.T) {