diff --git a/dojo/run.py b/dojo/run.py
index ba88cf3cd7a7147a754b3d6f6f3c4ed36ee95984..c3263f5544aba8b65edcba96ae1e773fac66bcde 100644
--- a/dojo/run.py
+++ b/dojo/run.py
@@ -16,6 +16,7 @@ class Entrypoint(object):
 
     def run(self, name, runner, config, env):
         # Build base config from core yml and jobs files.
+        config_dir = config
         base_config_path = os.path.join(config, 'config.yml')
         base_config = self._read_yaml(base_config_path) or {}
         if 'jobs' not in base_config:
@@ -31,7 +32,7 @@ class Entrypoint(object):
         config = deep_merge(base_config, env_config)
 
         # Build secrets by decrypting available EJSONs.
-        env_ejson_secrets_path = os.path.join(config, 'secrets.%s.ejson' % (env, ))
+        env_ejson_secrets_path = os.path.join(config_dir, 'secrets.%s.ejson' % (env, ))
         env_ejson_secrets = self._read_json(env_ejson_secrets_path)
         ejson_public_key = env_ejson_secrets['_public_key']
         ejson_private_key_path = os.path.join('/opt/ejson/keys/%s' % (ejson_public_key, ))