diff --git a/liminal/entity_schemas/compare.py b/liminal/entity_schemas/compare.py
index 1d43d0c..b20c1d3 100644
--- a/liminal/entity_schemas/compare.py
+++ b/liminal/entity_schemas/compare.py
@@ -232,6 +232,28 @@ def compare_entity_schemas(
                         )
                     )
             if benchling_schema_props != model.__schema_properties__:
+                needs_constraint_clear = (
+                    benchling_schema_props.constraint_fields
+                    != model.__schema_properties__.constraint_fields
+                    and len(benchling_schema_props.constraint_fields) > 0
+                )
+                if needs_constraint_clear:
+                    ops.append(
+                        CompareOperation(
+                            op=UpdateEntitySchema(
+                                model.__schema_properties__.warehouse_name,
+                                BaseSchemaProperties(constraint_fields=set()),
+                            ),
+                            reverse_op=UpdateEntitySchema(
+                                model.__schema_properties__.warehouse_name,
+                                BaseSchemaProperties(
+                                    **model.__schema_properties__.merge(
+                                        benchling_schema_props
+                                    )
+                                ),
+                            ),
+                        )
+                    )
                 ops.append(
                     CompareOperation(
                         op=UpdateEntitySchema(
@@ -244,7 +266,9 @@ def compare_entity_schemas(
                         ),
                         reverse_op=UpdateEntitySchema(
                             model.__schema_properties__.warehouse_name,
-                            BaseSchemaProperties(
+                            BaseSchemaProperties(constraint_fields=set())
+                            if needs_constraint_clear
+                            else BaseSchemaProperties(
                                 **model.__schema_properties__.merge(
                                     benchling_schema_props
                                 )
diff --git a/liminal/tests/test_entity_schema_compare.py b/liminal/tests/test_entity_schema_compare.py
index a13ad3b..0d0ddd5 100644
--- a/liminal/tests/test_entity_schema_compare.py
+++ b/liminal/tests/test_entity_schema_compare.py
@@ -361,13 +361,21 @@ def test_compare_benchling_schema_fields(  # type: ignore[no-untyped-def]
                 benchling_mismatch_constraint_fields
             )
             invalid_models = compare_entity_schemas(mock_benchling_sdk)
-            assert len(invalid_models["mock_entity"]) == 1
+            assert len(invalid_models["mock_entity"]) == 2
             assert isinstance(invalid_models["mock_entity"][0].op, UpdateEntitySchema)
-            assert invalid_models["mock_entity"][
+            clear_props_dict = invalid_models["mock_entity"][
                 0
-            ].op.update_props.constraint_fields == {
-                "string_field_req",
-                "enum_field",
+            ].op.update_props.model_dump(exclude_unset=True)
+            assert clear_props_dict == {"constraint_fields": set()}
+            assert isinstance(invalid_models["mock_entity"][1].op, UpdateEntitySchema)
+            update_props_dict = invalid_models["mock_entity"][
+                1
+            ].op.update_props.model_dump(exclude_unset=True)
+            assert update_props_dict == {
+                "constraint_fields": {
+                    "string_field_req",
+                    "enum_field",
+                },
             }
 
             # Test when the Benchling schema has different display naming fields