diff --git a/archiva-base/archiva-configuration/src/main/java/org/apache/maven/archiva/configuration/DefaultArchivaConfiguration.java b/archiva-base/archiva-configuration/src/main/java/org/apache/maven/archiva/configuration/DefaultArchivaConfiguration.java
index 5ca08dc85..4ea345016 100644
--- a/archiva-base/archiva-configuration/src/main/java/org/apache/maven/archiva/configuration/DefaultArchivaConfiguration.java
+++ b/archiva-base/archiva-configuration/src/main/java/org/apache/maven/archiva/configuration/DefaultArchivaConfiguration.java
@@ -172,6 +172,8 @@ public class DefaultArchivaConfiguration
 
             // Prevent duplicate repositories from showing up.
             config.getRepositories().clear();
+
+            registry.removeSubset( KEY + ".repositories" );
         }
 
         // Normalize the order fields in the proxy connectors.