diff --git a/django/db/backends/sqlite3/schema.py b/django/db/backends/sqlite3/schema.py
index 495714a894e..c5b428fc678 100644
--- a/django/db/backends/sqlite3/schema.py
+++ b/django/db/backends/sqlite3/schema.py
@@ -150,6 +150,9 @@ class DatabaseSchemaEditor(BaseDatabaseSchemaEditor):
             body.pop(old_field.name, None)
             mapping.pop(old_field.column, None)
             body[new_field.name] = new_field
+            rename_mapping[old_field.name] = new_field.name
+            if new_field.generated:
+                continue
             if old_field.null and not new_field.null:
                 if new_field.db_default is NOT_PROVIDED:
                     default = self.prepare_default(self.effective_default(new_field))
@@ -162,7 +165,6 @@ class DatabaseSchemaEditor(BaseDatabaseSchemaEditor):
                 mapping[new_field.column] = case_sql
             else:
                 mapping[new_field.column] = self.quote_name(old_field.column)
-            rename_mapping[old_field.name] = new_field.name
         # Remove any deleted fields
         if delete_field:
             del body[delete_field.name]
diff --git a/docs/releases/5.0.5.txt b/docs/releases/5.0.5.txt
index f8b66a59992..788753c8263 100644
--- a/docs/releases/5.0.5.txt
+++ b/docs/releases/5.0.5.txt
@@ -16,3 +16,7 @@ Bugfixes
 * Fixed a compatibility issue encountered in Python 3.11.9+ and 3.12.3+ when
   validating email max line lengths with content decoded using the
   ``surrogateescape`` error handling scheme (:ticket:`35361`).
+
+* Fixed a bug in Django 5.0 that caused a crash when applying migrations
+  including alterations to ``GeneratedField`` such as setting ``db_index=True``
+  on SQLite (:ticket:`35373`).
diff --git a/tests/schema/tests.py b/tests/schema/tests.py
index ff126d446a6..3a2947cf434 100644
--- a/tests/schema/tests.py
+++ b/tests/schema/tests.py
@@ -928,6 +928,39 @@ class SchemaTests(TransactionTestCase):
         self.assertEqual(obj.generated, "foo%")
         self.assertIs(obj.contains_foo, True)
 
+    @isolate_apps("schema")
+    @skipUnlessDBFeature("supports_stored_generated_columns")
+    def test_alter_generated_field(self):
+        class GeneratedFieldIndexedModel(Model):
+            number = IntegerField(default=1)
+            generated = GeneratedField(
+                expression=F("number"),
+                db_persist=True,
+                output_field=IntegerField(),
+            )
+
+            class Meta:
+                app_label = "schema"
+
+        with connection.schema_editor() as editor:
+            editor.create_model(GeneratedFieldIndexedModel)
+
+        old_field = GeneratedFieldIndexedModel._meta.get_field("generated")
+        new_field = GeneratedField(
+            expression=F("number"),
+            db_persist=True,
+            db_index=True,
+            output_field=IntegerField(),
+        )
+        new_field.contribute_to_class(GeneratedFieldIndexedModel, "generated")
+
+        with connection.schema_editor() as editor:
+            editor.alter_field(GeneratedFieldIndexedModel, old_field, new_field)
+
+        self.assertIn(
+            "generated", self.get_indexes(GeneratedFieldIndexedModel._meta.db_table)
+        )
+
     @isolate_apps("schema")
     def test_add_auto_field(self):
         class AddAutoFieldModel(Model):