diff --git a/tom/git.py b/tom/git.py
index b6c5ce5..4e9d634 100644
--- a/tom/git.py
+++ b/tom/git.py
@@ -123,6 +123,7 @@ def checkout(self, branch=None, tag=None, remote="upstream", new=False):
                 self.run_command("checkout", branch)
             # ensure we're on the tip of ref
             self.run_command("reset", "--hard", "FETCH_HEAD")
+        self.run_command("submodule", "update", "--init")
 
     def get_file(self, path):
         """Returns contents of a file as a single string"""