diff --git a/src/foremast/configs/outputs.py b/src/foremast/configs/outputs.py
index <HASH>..<HASH> 100644
--- a/src/foremast/configs/outputs.py
+++ b/src/foremast/configs/outputs.py
@@ -88,7 +88,9 @@ def write_variables(app_configs=None, out_file='', git_short=''):
             rendered_configs = json.loads(
                 get_template('configs/configs.json.j2', env=env, app=generated.app_name(), profile=instance_profile))
             json_configs[env] = dict(DeepChainMap(configs, rendered_configs))
-            for region in json_configs[env]['regions']:
+            region_list = configs['regions']
+            json_configs[env]['regions'] = region_list  # removes regions defined in templates but not configs.
+            for region in region_list:
                 region_config = json_configs[env][region]
                 json_configs[env][region] = dict(DeepChainMap(region_config, rendered_configs))
         else:
overrides regions in templates with regions in configs