diff --git a/django/core/management/commands/makemigrations.py b/django/core/management/commands/makemigrations.py
index 839592a22ad..38ed9db4737 100644
--- a/django/core/management/commands/makemigrations.py
+++ b/django/core/management/commands/makemigrations.py
@@ -94,7 +94,11 @@ class Command(BaseCommand):
             return
 
         # Detect changes
-        changes = autodetector.changes(graph=loader.graph, trim_to_apps=app_labels or None)
+        changes = autodetector.changes(
+            graph=loader.graph,
+            trim_to_apps=app_labels or None,
+            convert_apps=app_labels or None,
+        )
 
         # No changes? Tell them.
         if not changes and self.verbosity >= 1:
diff --git a/django/db/migrations/autodetector.py b/django/db/migrations/autodetector.py
index 3e3dc242d20..6ed6edc38ee 100644
--- a/django/db/migrations/autodetector.py
+++ b/django/db/migrations/autodetector.py
@@ -28,13 +28,13 @@ class MigrationAutodetector(object):
         self.to_state = to_state
         self.questioner = questioner or MigrationQuestioner()
 
-    def changes(self, graph, trim_to_apps=None):
+    def changes(self, graph, trim_to_apps=None, convert_apps=None):
         """
         Main entry point to produce a list of appliable changes.
         Takes a graph to base names on and an optional set of apps
         to try and restrict to (restriction is not guaranteed)
         """
-        changes = self._detect_changes()
+        changes = self._detect_changes(convert_apps)
         changes = self.arrange_for_graph(changes, graph)
         if trim_to_apps:
             changes = self._trim_to_apps(changes, trim_to_apps)
@@ -77,7 +77,7 @@ class MigrationAutodetector(object):
             fields_def.append(deconstruction)
         return fields_def
 
-    def _detect_changes(self):
+    def _detect_changes(self, convert_apps=None):
         """
         Returns a dict of migration plans which will achieve the
         change from from_state to to_state. The dict has app labels
@@ -105,7 +105,10 @@ class MigrationAutodetector(object):
         self.new_model_keys = []
         for al, mn in sorted(self.to_state.models.keys()):
             model = self.new_apps.get_model(al, mn)
-            if not model._meta.proxy and model._meta.managed and al not in self.from_state.real_apps:
+            if not model._meta.proxy and model._meta.managed and (
+                al not in self.from_state.real_apps or
+                (convert_apps and al in convert_apps)
+            ):
                 self.new_model_keys.append((al, mn))
 
         # Renames have to come first
@@ -376,6 +379,14 @@ class MigrationAutodetector(object):
                 else:
                     dep_app_label = field.rel.to._meta.app_label
                     dep_object_name = field.rel.to._meta.object_name
+                dependencies = [(dep_app_label, dep_object_name, None, True)]
+                if getattr(field.rel, "through", None) and not field.rel.through._meta.auto_created:
+                    dependencies.append((
+                        field.rel.through._meta.app_label,
+                        field.rel.through._meta.object_name,
+                        None,
+                        True
+                    ))
                 # Make operation
                 self.add_operation(
                     app_label,
@@ -384,9 +395,7 @@ class MigrationAutodetector(object):
                         name=name,
                         field=field,
                     ),
-                    dependencies=[
-                        (dep_app_label, dep_object_name, None, True),
-                    ]
+                    dependencies=list(set(dependencies)),
                 )
             # Generate other opns
             if unique_together:
diff --git a/tests/migrations/test_autodetector.py b/tests/migrations/test_autodetector.py
index e10060d251f..d6a908143dd 100644
--- a/tests/migrations/test_autodetector.py
+++ b/tests/migrations/test_autodetector.py
@@ -79,7 +79,7 @@ class AutodetectorTests(TestCase):
     def assertNumberMigrations(self, changes, app_label, number):
         if len(changes.get(app_label, [])) != number:
             self.fail("Incorrect number of migrations (%s) for %s (expected %s)\n%s" % (
-                len(changes[app_label]),
+                len(changes.get(app_label, [])),
                 app_label,
                 number,
                 self.repr_changes(changes),
@@ -706,6 +706,20 @@ class AutodetectorTests(TestCase):
         self.assertEqual(action.__class__.__name__, "AddField")
         self.assertEqual(action.name, "publishers")
 
+    def test_create_with_through_model(self):
+        """
+        Adding a m2m with a through model and the models that use it should
+        be ordered correctly.
+        """
+        before = self.make_project_state([])
+        after = self.make_project_state([self.author_with_m2m_through, self.publisher, self.contract])
+        autodetector = MigrationAutodetector(before, after)
+        changes = autodetector._detect_changes()
+        # Right number of migrations?
+        self.assertNumberMigrations(changes, "testapp", 1)
+        # Right actions in right order?
+        self.assertOperationTypes(changes, "testapp", 0, ["CreateModel", "CreateModel", "CreateModel", "AddField", "AddField"])
+
     def test_many_to_many_removed_before_through_model(self):
         """
         Removing a ManyToManyField and the "through" model in the same change must remove