diff --git a/fdroidserver/common.py b/fdroidserver/common.py
index 7533149e..4f3b35ee 100644
--- a/fdroidserver/common.py
+++ b/fdroidserver/common.py
@@ -864,16 +864,16 @@ def prepare_source(vcs, app, build, build_dir, srclib_dir, extlib_dir, onserver=
     logging.info("Getting source for revision " + build['commit'])
     vcs.gotorevision(build['commit'])
 
-    # Check that a subdir (if we're using one) exists. This has to happen
-    # after the checkout, since it might not exist elsewhere
-    if not os.path.exists(root_dir):
-        raise BuildException('Missing subdir ' + root_dir)
-
     # Initialise submodules if requred
     if build['submodules']:
         logging.info("Initialising submodules")
         vcs.initsubmodules()
 
+    # Check that a subdir (if we're using one) exists. This has to happen
+    # after the checkout, since it might not exist elsewhere
+    if not os.path.exists(root_dir):
+        raise BuildException('Missing subdir ' + root_dir)
+
     # Run an init command if one is required
     if 'init' in build:
         cmd = replace_config_vars(build['init'])