diff --git a/django/db/models/query.py b/django/db/models/query.py
index 46733c8cb0..0a7156d8b6 100644
--- a/django/db/models/query.py
+++ b/django/db/models/query.py
@@ -1252,8 +1252,9 @@ class QuerySet(AltersData):
                 new_order_by.append(col)
         query.order_by = tuple(new_order_by)
 
-        # Clear any annotations so that they won't be present in subqueries.
-        query.annotations = {}
+        # Clear SELECT clause as all annotation references were inlined by
+        # add_update_values() already.
+        query.clear_select_clause()
         with transaction.mark_for_rollback_on_error(using=self.db):
             rows = query.get_compiler(self.db).execute_sql(ROW_COUNT)
         self._result_cache = None
diff --git a/docs/releases/5.2.1.txt b/docs/releases/5.2.1.txt
index a79d61c60a..19d14bbddf 100644
--- a/docs/releases/5.2.1.txt
+++ b/docs/releases/5.2.1.txt
@@ -51,3 +51,7 @@ Bugfixes
 
 * Fixed a regression in Django 5.2 that caused a crash when serializing email
   alternatives or attachments due to named tuple mismatches (:ticket:`36309`).
+
+* Fixed a regression in Django 5.2 that caused a crash when using ``update()``
+  on a ``QuerySet`` filtered against a related model and including references
+  to annotations through ``values()`` (:ticket:`36360`).
diff --git a/tests/update/tests.py b/tests/update/tests.py
index 079e00818a..a365dc00c5 100644
--- a/tests/update/tests.py
+++ b/tests/update/tests.py
@@ -256,6 +256,13 @@ class AdvancedTests(TestCase):
         Bar.objects.annotate(abs_id=Abs("m2m_foo")).order_by("-abs_id").update(x=4)
         self.assertEqual(Bar.objects.get().x, 4)
 
+    def test_update_values_annotation(self):
+        RelatedPoint.objects.annotate(abs_id=Abs("id")).filter(
+            data__is_active=False
+        ).values("id", "abs_id").update(data=self.d0)
+        self.r1.refresh_from_db(fields=["data"])
+        self.assertEqual(self.r1.data, self.d0)
+
     def test_update_negated_f(self):
         DataPoint.objects.update(is_active=~F("is_active"))
         self.assertCountEqual(