diff --git a/dhis-2/dhis-services/dhis-service-core/src/main/java/org/hisp/dhis/common/hibernate/HibernateIdentifiableObjectStore.java b/dhis-2/dhis-services/dhis-service-core/src/main/java/org/hisp/dhis/common/hibernate/HibernateIdentifiableObjectStore.java
index 936812e8c0c6..14abd7a1d48d 100644
--- a/dhis-2/dhis-services/dhis-service-core/src/main/java/org/hisp/dhis/common/hibernate/HibernateIdentifiableObjectStore.java
+++ b/dhis-2/dhis-services/dhis-service-core/src/main/java/org/hisp/dhis/common/hibernate/HibernateIdentifiableObjectStore.java
@@ -33,6 +33,7 @@
 import static org.hisp.dhis.query.JpaQueryUtils.generateHqlQueryForSharingCheck;
 
 import jakarta.persistence.EntityManager;
+import jakarta.persistence.FlushModeType;
 import jakarta.persistence.TypedQuery;
 import jakarta.persistence.criteria.CriteriaBuilder;
 import jakarta.persistence.criteria.CriteriaQuery;
@@ -919,7 +920,14 @@ public List<T> findByCreatedBy(@Nonnull UserDetails user) {
   }
 
   /**
-   * Look up objects which have property createdBy or lastUpdatedBy linked to given {@link User}
+   * Look up objects which have property createdBy or lastUpdatedBy linked to given {@link User}.
+   *
+   * <p>Runs with {@link FlushModeType#COMMIT}, so the JPA auto-flush (a full-session dirty-check)
+   * is skipped before this query. This is safe for the current caller (the read-only deletion veto
+   * phase, which runs before any deletion handler writes), and avoids a per-query flush that
+   * dominates the cost when a large object graph is in the session. If a future caller reads within
+   * a transaction and must observe earlier un-flushed changes, change this method to accept a
+   * flush-mode parameter rather than relaxing the mode for everyone.
    *
    * @param user the {@link User} for filtering
    * @return TRUE of objects found. FALSE otherwise.
@@ -939,7 +947,12 @@ public boolean existsByUser(@Nonnull User user, final Set<String> checkPropertie
       return false;
     }
     query.where(builder.or(predicates.toArray(new Predicate[0])));
-    return !entityManager.createQuery(query).setMaxResults(1).getResultList().isEmpty();
+    return !entityManager
+        .createQuery(query)
+        .setFlushMode(FlushModeType.COMMIT)
+        .setMaxResults(1)
+        .getResultList()
+        .isEmpty();
   }
 
   /**
diff --git a/dhis-2/dhis-test-integration/src/test/java/org/hisp/dhis/dataelement/DataElementStoreTest.java b/dhis-2/dhis-test-integration/src/test/java/org/hisp/dhis/dataelement/DataElementStoreTest.java
index 5b0d9075db57..4261b6ed6e02 100644
--- a/dhis-2/dhis-test-integration/src/test/java/org/hisp/dhis/dataelement/DataElementStoreTest.java
+++ b/dhis-2/dhis-test-integration/src/test/java/org/hisp/dhis/dataelement/DataElementStoreTest.java
@@ -347,6 +347,7 @@ void testExistsByUser() {
     DataElement dataElementA = createDataElement('A');
     dataElementA.setCreatedBy(userA);
     dataElementStore.save(dataElementA);
+    entityManager.flush();
     assertTrue(dataElementStore.existsByUser(userA, Set.of("createdBy")));
     assertFalse(dataElementStore.existsByUser(userB, Set.of("createdBy")));
 
diff --git a/dhis-2/dhis-test-integration/src/test/java/org/hisp/dhis/user/UserServiceTest.java b/dhis-2/dhis-test-integration/src/test/java/org/hisp/dhis/user/UserServiceTest.java
index f0fdd64f3b1b..c589654ec99f 100644
--- a/dhis-2/dhis-test-integration/src/test/java/org/hisp/dhis/user/UserServiceTest.java
+++ b/dhis-2/dhis-test-integration/src/test/java/org/hisp/dhis/user/UserServiceTest.java
@@ -194,6 +194,7 @@ void testDeleteCreatedByUser() {
     DataElement dataElement = createDataElement('A');
     dataElement.setCreatedBy(userA);
     idObjectManager.save(dataElement);
+    entityManager.flush();
 
     assertThrows(DeleteNotAllowedException.class, () -> userService.deleteUser(userA));
   }
@@ -208,6 +209,7 @@ void testDeleteLastUpdatedByUser() {
 
     dataElement.setDescription("Updated");
     idObjectManager.update(dataElement);
+    entityManager.flush();
 
     assertThrows(DeleteNotAllowedException.class, () -> userService.deleteUser(userA));
   }