diff --git a/plugins/catalog-backend-module-incremental-ingestion/src/database/IncrementalIngestionDatabaseManager.test.ts b/plugins/catalog-backend-module-incremental-ingestion/src/database/IncrementalIngestionDatabaseManager.test.ts
index 155b45cacb..91975edfb5 100644
--- a/plugins/catalog-backend-module-incremental-ingestion/src/database/IncrementalIngestionDatabaseManager.test.ts
+++ b/plugins/catalog-backend-module-incremental-ingestion/src/database/IncrementalIngestionDatabaseManager.test.ts
@@ -122,123 +122,123 @@ describe.each(databases.eachSupportedId())(
       expect(typeof result.total).toBe('number');
     });
 
-  it('createMarkEntities handles existing and new refs correctly', async () => {
-    const knex = await databases.init(databaseId);
-    await knex.migrate.latest({ directory: migrationsDir });
+    it('createMarkEntities handles existing and new refs correctly', async () => {
+      const knex = await databases.init(databaseId);
+      await knex.migrate.latest({ directory: migrationsDir });
 
-    const manager = new IncrementalIngestionDatabaseManager({ client: knex });
-    const { ingestionId } = (await manager.createProviderIngestionRecord(
-      'testProvider',
-    ))!;
+      const manager = new IncrementalIngestionDatabaseManager({ client: knex });
+      const { ingestionId } = (await manager.createProviderIngestionRecord(
+        'testProvider',
+      ))!;
 
-    const markId1 = uuid();
-    await manager.createMark({
-      record: {
-        id: markId1,
-        ingestion_id: ingestionId,
-        sequence: 1,
-        cursor: { data: 1 },
-      },
+      const markId1 = uuid();
+      await manager.createMark({
+        record: {
+          id: markId1,
+          ingestion_id: ingestionId,
+          sequence: 1,
+          cursor: { data: 1 },
+        },
+      });
+
+      const makeEntity = (name: string): DeferredEntity => ({
+        entity: {
+          apiVersion: 'backstage.io/v1alpha1',
+          kind: 'Component',
+          metadata: { namespace: 'default', name },
+        },
+      });
+
+      // First batch: create 3 entities
+      await manager.createMarkEntities(markId1, [
+        makeEntity('a'),
+        makeEntity('b'),
+        makeEntity('c'),
+      ]);
+
+      const rows1 = await knex('ingestion_mark_entities').select('ref');
+      expect(rows1).toHaveLength(3);
+
+      // Second batch with overlap: b and c already exist, d is new.
+      // Existing refs should be updated to the new mark, new refs inserted.
+      const markId2 = uuid();
+      await manager.createMark({
+        record: {
+          id: markId2,
+          ingestion_id: ingestionId,
+          sequence: 2,
+          cursor: { data: 2 },
+        },
+      });
+
+      await manager.createMarkEntities(markId2, [
+        makeEntity('b'),
+        makeEntity('c'),
+        makeEntity('d'),
+      ]);
+
+      const rows2 = await knex('ingestion_mark_entities')
+        .select('ref', 'ingestion_mark_id')
+        .orderBy('ref');
+      expect(rows2).toHaveLength(4);
+
+      // a stays on markId1, b and c moved to markId2, d is new on markId2
+      expect(
+        rows2.find(r => r.ref === 'component:default/a')?.ingestion_mark_id,
+      ).toBe(markId1);
+      expect(
+        rows2.find(r => r.ref === 'component:default/b')?.ingestion_mark_id,
+      ).toBe(markId2);
+      expect(
+        rows2.find(r => r.ref === 'component:default/c')?.ingestion_mark_id,
+      ).toBe(markId2);
+      expect(
+        rows2.find(r => r.ref === 'component:default/d')?.ingestion_mark_id,
+      ).toBe(markId2);
     });
 
-    const makeEntity = (name: string): DeferredEntity => ({
-      entity: {
-        apiVersion: 'backstage.io/v1alpha1',
-        kind: 'Component',
-        metadata: { namespace: 'default', name },
-      },
+    it('deleteEntityRecordsByRef removes matching refs', async () => {
+      const knex = await databases.init(databaseId);
+      await knex.migrate.latest({ directory: migrationsDir });
+
+      const manager = new IncrementalIngestionDatabaseManager({ client: knex });
+      const { ingestionId } = (await manager.createProviderIngestionRecord(
+        'testProvider',
+      ))!;
+
+      const markId = uuid();
+      await manager.createMark({
+        record: {
+          id: markId,
+          ingestion_id: ingestionId,
+          sequence: 1,
+          cursor: { data: 1 },
+        },
+      });
+
+      const makeEntity = (name: string): DeferredEntity => ({
+        entity: {
+          apiVersion: 'backstage.io/v1alpha1',
+          kind: 'Component',
+          metadata: { namespace: 'default', name },
+        },
+      });
+
+      await manager.createMarkEntities(markId, [
+        makeEntity('x'),
+        makeEntity('y'),
+        makeEntity('z'),
+      ]);
+
+      // Delete two of the three
+      await manager.deleteEntityRecordsByRef([
+        { entityRef: 'component:default/x' },
+        { entityRef: 'component:default/z' },
+      ]);
+
+      const remaining = await knex('ingestion_mark_entities').select('ref');
+      expect(remaining).toHaveLength(1);
+      expect(remaining[0].ref).toBe('component:default/y');
     });
-
-    // First batch: create 3 entities
-    await manager.createMarkEntities(markId1, [
-      makeEntity('a'),
-      makeEntity('b'),
-      makeEntity('c'),
-    ]);
-
-    const rows1 = await knex('ingestion_mark_entities').select('ref');
-    expect(rows1).toHaveLength(3);
-
-    // Second batch with overlap: b and c already exist, d is new.
-    // Existing refs should be updated to the new mark, new refs inserted.
-    const markId2 = uuid();
-    await manager.createMark({
-      record: {
-        id: markId2,
-        ingestion_id: ingestionId,
-        sequence: 2,
-        cursor: { data: 2 },
-      },
-    });
-
-    await manager.createMarkEntities(markId2, [
-      makeEntity('b'),
-      makeEntity('c'),
-      makeEntity('d'),
-    ]);
-
-    const rows2 = await knex('ingestion_mark_entities')
-      .select('ref', 'ingestion_mark_id')
-      .orderBy('ref');
-    expect(rows2).toHaveLength(4);
-
-    // a stays on markId1, b and c moved to markId2, d is new on markId2
-    expect(
-      rows2.find(r => r.ref === 'component:default/a')?.ingestion_mark_id,
-    ).toBe(markId1);
-    expect(
-      rows2.find(r => r.ref === 'component:default/b')?.ingestion_mark_id,
-    ).toBe(markId2);
-    expect(
-      rows2.find(r => r.ref === 'component:default/c')?.ingestion_mark_id,
-    ).toBe(markId2);
-    expect(
-      rows2.find(r => r.ref === 'component:default/d')?.ingestion_mark_id,
-    ).toBe(markId2);
-  });
-
-  it('deleteEntityRecordsByRef removes matching refs', async () => {
-    const knex = await databases.init(databaseId);
-    await knex.migrate.latest({ directory: migrationsDir });
-
-    const manager = new IncrementalIngestionDatabaseManager({ client: knex });
-    const { ingestionId } = (await manager.createProviderIngestionRecord(
-      'testProvider',
-    ))!;
-
-    const markId = uuid();
-    await manager.createMark({
-      record: {
-        id: markId,
-        ingestion_id: ingestionId,
-        sequence: 1,
-        cursor: { data: 1 },
-      },
-    });
-
-    const makeEntity = (name: string): DeferredEntity => ({
-      entity: {
-        apiVersion: 'backstage.io/v1alpha1',
-        kind: 'Component',
-        metadata: { namespace: 'default', name },
-      },
-    });
-
-    await manager.createMarkEntities(markId, [
-      makeEntity('x'),
-      makeEntity('y'),
-      makeEntity('z'),
-    ]);
-
-    // Delete two of the three
-    await manager.deleteEntityRecordsByRef([
-      { entityRef: 'component:default/x' },
-      { entityRef: 'component:default/z' },
-    ]);
-
-    const remaining = await knex('ingestion_mark_entities').select('ref');
-    expect(remaining).toHaveLength(1);
-    expect(remaining[0].ref).toBe('component:default/y');
-  });
-},
+  },
 );
diff --git a/plugins/catalog-backend-module-incremental-ingestion/src/database/IncrementalIngestionDatabaseManager.ts b/plugins/catalog-backend-module-incremental-ingestion/src/database/IncrementalIngestionDatabaseManager.ts
index 78dc646d72..ecf821364f 100644
--- a/plugins/catalog-backend-module-incremental-ingestion/src/database/IncrementalIngestionDatabaseManager.ts
+++ b/plugins/catalog-backend-module-incremental-ingestion/src/database/IncrementalIngestionDatabaseManager.ts
@@ -94,9 +94,11 @@ export class IncrementalIngestionDatabaseManager {
     const allIds = ids.map(entry => entry.id);
 
     if (this.client.client.config.client === 'pg') {
-      return await tx('ingestion_mark_entities')
-        .delete()
-        .whereRaw('?? = ANY(?)', ['id', allIds]);
+      return await this.whereInArray(
+        tx('ingestion_mark_entities').delete(),
+        'id',
+        allIds,
+      );
     }
 
     let deleted = 0;