diff --git a/django/db/backends/sqlite3/schema.py b/django/db/backends/sqlite3/schema.py
index d1b113f1b9..78d88c7dd9 100644
--- a/django/db/backends/sqlite3/schema.py
+++ b/django/db/backends/sqlite3/schema.py
@@ -361,12 +361,21 @@ class DatabaseSchemaEditor(BaseDatabaseSchemaEditor):
         # Rebuild tables with FKs pointing to this field if the PK type changed.
         if old_field.primary_key and new_field.primary_key and old_type != new_type:
             related_models = set()
-            for remote_field in new_field.model._meta.related_objects:
+            opts = new_field.model._meta
+            for remote_field in opts.related_objects:
                 # Ignore self-relationship since the table was already rebuilt.
                 if remote_field.related_model == model:
                     continue
                 if not remote_field.many_to_many:
                     related_models.add(remote_field.related_model)
+                elif remote_field.through._meta.auto_created:
+                    related_models.add(remote_field.through)
+            for many_to_many in opts.many_to_many:
+                # Ignore self-relationship since the table was already rebuilt.
+                if many_to_many.related_model == model:
+                    continue
+                if many_to_many.remote_field.through._meta.auto_created:
+                    related_models.add(many_to_many.remote_field.through)
             for related_model in related_models:
                 self._remake_table(related_model)
 
diff --git a/tests/migrations/test_operations.py b/tests/migrations/test_operations.py
index 162a14d529..051b8036b5 100644
--- a/tests/migrations/test_operations.py
+++ b/tests/migrations/test_operations.py
@@ -1275,6 +1275,16 @@ class OperationTests(OperationTestBase):
         Tests the AlterField operation on primary keys changes any FKs pointing to it.
         """
         project_state = self.set_up_test_model("test_alflpkfk", related_model=True)
+        project_state = self.apply_operations('test_alflpkfk', project_state, [
+            migrations.CreateModel('Stable', fields=[
+                ('ponies', models.ManyToManyField('Pony')),
+            ]),
+            migrations.AddField(
+                'Pony',
+                'stables',
+                models.ManyToManyField('Stable'),
+            ),
+        ])
         # Test the state alteration
         operation = migrations.AlterField("Pony", "id", models.FloatField(primary_key=True))
         new_state = project_state.clone()
@@ -1294,8 +1304,26 @@ class OperationTests(OperationTestBase):
                     for c in connection.introspection.get_table_description(cursor, "test_alflpkfk_rider")
                     if c.name == "pony_id"
                 ][0]
+                m2m_fk_type, m2m_fk_null = [
+                    (c.type_code, c.null_ok)
+                    for c in connection.introspection.get_table_description(
+                        cursor,
+                        'test_alflpkfk_pony_stables',
+                    ) if c.name == 'pony_id'
+                ][0]
+                remote_m2m_fk_type, remote_m2m_fk_null = [
+                    (c.type_code, c.null_ok)
+                    for c in connection.introspection.get_table_description(
+                        cursor,
+                        'test_alflpkfk_stable_ponies',
+                    ) if c.name == 'pony_id'
+                ][0]
             self.assertEqual(id_type, fk_type)
+            self.assertEqual(id_type, m2m_fk_type)
+            self.assertEqual(id_type, remote_m2m_fk_type)
             self.assertEqual(id_null, fk_null)
+            self.assertEqual(id_null, m2m_fk_null)
+            self.assertEqual(id_null, remote_m2m_fk_null)
 
         assertIdTypeEqualsFkType()
         # Test the database alteration