diff --git a/jOOQ-codegen-gradle/src/main/java/org/jooq/codegen/gradle/NamedConfiguration.java b/jOOQ-codegen-gradle/src/main/java/org/jooq/codegen/gradle/NamedConfiguration.java
index c69a65edb7..5761db41d0 100644
--- a/jOOQ-codegen-gradle/src/main/java/org/jooq/codegen/gradle/NamedConfiguration.java
+++ b/jOOQ-codegen-gradle/src/main/java/org/jooq/codegen/gradle/NamedConfiguration.java
@@ -100,11 +100,15 @@ public class NamedConfiguration {
 
     void configuration0(Configuration configuration) {
         if (!unnamed)
-            MiniJAXB.append(this.configuration, project.getExtensions().getByType(CodegenPluginExtension.class).defaultConfiguration().configuration);
+            MiniJAXB.append(this.configuration, copy(project.getExtensions().getByType(CodegenPluginExtension.class).defaultConfiguration().configuration));
 
         MiniJAXB.append(this.configuration, configuration);
     }
 
+    static Configuration copy(Configuration configuration) {
+        return MiniJAXB.unmarshal(MiniJAXB.marshal(configuration), Configuration.class);
+    }
+
     public void configuration(Action<ConfigurationExtension> action) {
         ConfigurationExtension c = objects.newInstance(ConfigurationExtension.class, objects);
         action.execute(c);