diff --git a/synapse/config/_base.py b/synapse/config/_base.py
index 1a6784a714c5dfd84f09aea607764cfbbf390e8c..8a75c48733cb9105a389defea736f90fd94f5d49 100644
--- a/synapse/config/_base.py
+++ b/synapse/config/_base.py
@@ -182,7 +182,7 @@ class Config(object):
                             ) % (entry_path, )
                             continue
 
-                        files.add(config_path)
+                        files.append(entry_path)
 
                     config_files.extend(sorted(files))
                 else: