diff --git a/packages/ketcher-core/src/domain/serializers/ket/ketSerializer.ts b/packages/ketcher-core/src/domain/serializers/ket/ketSerializer.ts
index b9f19a5eef..e117fd0eca 100644
--- a/packages/ketcher-core/src/domain/serializers/ket/ketSerializer.ts
+++ b/packages/ketcher-core/src/domain/serializers/ket/ketSerializer.ts
@@ -332,6 +332,14 @@ export class KetSerializer implements Serializer<Struct> {
       fileContentForMicromolecules[template.$ref] = undefined;
     });
 
+    Object.entries(
+      fileContentForMicromolecules as IKetMacromoleculesContent,
+    ).forEach(([key, value]) => {
+      if (value?.type === KetTemplateType.AMBIGUOUS_MONOMER_TEMPLATE) {
+        fileContentForMicromolecules[key] = undefined;
+      }
+    });
+
     return fileContentForMicromolecules;
   }