diff --git a/packages/twenty-server/src/database/commands/upgrade-version-command/2-16/2-16-workspace-command-1799100000000-backfill-search-field-metadata.command.ts b/packages/twenty-server/src/database/commands/upgrade-version-command/2-16/2-16-workspace-command-1799100000000-backfill-search-field-metadata.command.ts
index e414063e7b..9ed24c1465 100644
--- a/packages/twenty-server/src/database/commands/upgrade-version-command/2-16/2-16-workspace-command-1799100000000-backfill-search-field-metadata.command.ts
+++ b/packages/twenty-server/src/database/commands/upgrade-version-command/2-16/2-16-workspace-command-1799100000000-backfill-search-field-metadata.command.ts
@@ -34,11 +34,16 @@ export class BackfillSearchFieldMetadataCommand extends ProvisionedWorkspaceComm
     const isDryRun = options.dryRun ?? false;
 
     // The migration runner only invalidates the flat-maps keys a migration touched,
-    // so during a cross-version upgrade earlier commands can leave this map stale.
-    // A stale map breaks the existing-rows dedupe below and re-inserts rows,
-    // tripping IDX_SEARCH_FIELD_METADATA_OBJECT_FIELD_UNIQUE. Recompute from the
-    // database before deriving the create-set.
+    // so during a cross-version upgrade earlier commands can leave these maps stale.
+    // The existing-rows dedupe below compares (objectMetadataId, fieldMetadataId)
+    // pairs across maps: candidate ids resolved from a stale object/field map won't
+    // match the fresh search map's ids, so already-created rows are re-emitted and
+    // the runner (which re-resolves universal identifiers against fresh maps) trips
+    // IDX_SEARCH_FIELD_METADATA_OBJECT_FIELD_UNIQUE. Recompute every map the dedupe
+    // depends on from the database before deriving the create-set.
     await this.workspaceCacheService.invalidateAndRecompute(workspaceId, [
+      'flatObjectMetadataMaps',
+      'flatFieldMetadataMaps',
       'flatSearchFieldMetadataMaps',
     ]);
 
diff --git a/packages/twenty-server/src/database/commands/upgrade-version-command/2-16/utils/__tests__/build-search-field-metadata-backfill-operations.util.spec.ts b/packages/twenty-server/src/database/commands/upgrade-version-command/2-16/utils/__tests__/build-search-field-metadata-backfill-operations.util.spec.ts
index 4955883268..ff6e684014 100644
--- a/packages/twenty-server/src/database/commands/upgrade-version-command/2-16/utils/__tests__/build-search-field-metadata-backfill-operations.util.spec.ts
+++ b/packages/twenty-server/src/database/commands/upgrade-version-command/2-16/utils/__tests__/build-search-field-metadata-backfill-operations.util.spec.ts
@@ -1,4 +1,7 @@
-import { TWENTY_STANDARD_APPLICATION_UNIVERSAL_IDENTIFIER } from 'twenty-shared/application';
+import {
+  getSearchFieldUniversalIdentifier,
+  TWENTY_STANDARD_APPLICATION_UNIVERSAL_IDENTIFIER,
+} from 'twenty-shared/application';
 import { FieldMetadataType } from 'twenty-shared/types';
 
 import { buildSearchFieldMetadataBackfillOperations } from 'src/database/commands/upgrade-version-command/2-16/utils/build-search-field-metadata-backfill-operations.util';
@@ -622,6 +625,54 @@ describe('buildSearchFieldMetadataBackfillOperations', () => {
     ).toHaveLength(0);
   });
 
+  it('skips a row whose deterministic universal identifier already exists even when the existing row carries stale metadata ids', () => {
+    const { customObject, nameField, nameDescriptionField, searchVectorField } =
+      buildCustomObjectFixture();
+
+    // Simulates a retry after a partial run during a cross-version upgrade: the
+    // previously committed row still points at the ids the metadata had at insert
+    // time, while the object/field maps now expose new ids (id churn from earlier
+    // upgrade commands). The (objectMetadataId, fieldMetadataId) dedupe misses the
+    // pair, but the deterministic universal identifier is unchanged and must
+    // prevent re-emitting the row.
+    const existingSearchFieldMetadata = buildSearchFieldMetadata({
+      id: 'existing-search-field-id',
+      universalIdentifier: getSearchFieldUniversalIdentifier({
+        applicationUniversalIdentifier:
+          CUSTOM_APPLICATION_UNIVERSAL_IDENTIFIER,
+        fieldMetadataUniversalIdentifier: nameField.universalIdentifier,
+      }),
+      objectMetadataId: 'stale-object-metadata-id',
+      fieldMetadataId: 'stale-field-metadata-id',
+      objectMetadataUniversalIdentifier: customObject.universalIdentifier,
+      fieldMetadataUniversalIdentifier: nameField.universalIdentifier,
+      applicationUniversalIdentifier: CUSTOM_APPLICATION_UNIVERSAL_IDENTIFIER,
+    });
+
+    const { flatSearchFieldMetadatasToCreateByApplicationUniversalIdentifier } =
+      buildSearchFieldMetadataBackfillOperations({
+        flatObjectMetadataMaps: buildFlatObjectMetadataMaps([customObject]),
+        flatFieldMetadataMaps: buildFlatFieldMetadataMaps([
+          nameField,
+          nameDescriptionField,
+          searchVectorField,
+        ]),
+        flatSearchFieldMetadataMaps: buildFlatSearchFieldMetadataMaps([
+          existingSearchFieldMetadata,
+        ]),
+        standardFlatSearchFieldMetadataMaps: buildFlatSearchFieldMetadataMaps(
+          [],
+        ),
+        customApplicationId: CUSTOM_APPLICATION_ID,
+      });
+
+    expect(
+      Object.keys(
+        flatSearchFieldMetadatasToCreateByApplicationUniversalIdentifier,
+      ),
+    ).toHaveLength(0);
+  });
+
   it('skips a custom object whose name field is not a searchable type', () => {
     const customObjectId = 'relation-name-object-id';
     const customObjectUniversalIdentifier = 'relation-name-object-uid';
diff --git a/packages/twenty-server/src/database/commands/upgrade-version-command/2-16/utils/build-search-field-metadata-backfill-operations.util.ts b/packages/twenty-server/src/database/commands/upgrade-version-command/2-16/utils/build-search-field-metadata-backfill-operations.util.ts
index 41220b32e6..5631940e82 100644
--- a/packages/twenty-server/src/database/commands/upgrade-version-command/2-16/utils/build-search-field-metadata-backfill-operations.util.ts
+++ b/packages/twenty-server/src/database/commands/upgrade-version-command/2-16/utils/build-search-field-metadata-backfill-operations.util.ts
@@ -94,16 +94,32 @@ export const buildSearchFieldMetadataBackfillOperations = ({
       return;
     }
 
-    candidateSearchFieldMetadataKeys.add(searchFieldMetadataKey);
-
-    flatSearchFieldMetadatasToCreate.push(
-      buildFlatSearchFieldMetadataForField({
+    const universalFlatSearchFieldMetadata = buildFlatSearchFieldMetadataForField(
+      {
         flatObjectMetadata,
         flatFieldMetadata,
         tsVectorFlatFieldMetadata,
         position,
-      }),
+      },
     );
+
+    // Second dedupe layer, immune to metadata-id churn: rows created by a previous
+    // partial run of this command carry the same deterministic universal identifier
+    // (unique per workspace). The id-based check above can miss them when earlier
+    // upgrade commands recreated objects/fields under new ids.
+    if (
+      isDefined(
+        flatSearchFieldMetadataMaps.byUniversalIdentifier[
+          universalFlatSearchFieldMetadata.universalIdentifier
+        ],
+      )
+    ) {
+      return;
+    }
+
+    candidateSearchFieldMetadataKeys.add(searchFieldMetadataKey);
+
+    flatSearchFieldMetadatasToCreate.push(universalFlatSearchFieldMetadata);
   };
 
   // Standard objects: mirror exactly what provisioning/standard-sync creates.