diff --git a/core/deployment/src/main/java/io/quarkus/deployment/steps/ConfigBuildSteps.java b/core/deployment/src/main/java/io/quarkus/deployment/steps/ConfigBuildSteps.java
index 478b4b9d13ff4..975071dad0eb1 100644
--- a/core/deployment/src/main/java/io/quarkus/deployment/steps/ConfigBuildSteps.java
+++ b/core/deployment/src/main/java/io/quarkus/deployment/steps/ConfigBuildSteps.java
@@ -15,6 +15,7 @@
 import io.quarkus.deployment.builditem.StaticInitConfigBuilderBuildItem;
 import io.quarkus.deployment.builditem.nativeimage.RuntimeInitializedClassBuildItem;
 import io.quarkus.deployment.builditem.nativeimage.ServiceProviderBuildItem;
+import io.quarkus.deployment.pkg.steps.NativeOrNativeSourcesBuild;
 import io.quarkus.deployment.util.ServiceUtil;
 import io.quarkus.runtime.configuration.SystemOnlySourcesConfigBuilder;
 import io.quarkus.runtime.graal.InetRunTime;
@@ -62,6 +63,16 @@ void systemOnlySources(BuildProducer<StaticInitConfigBuilderBuildItem> staticIni
         runTimeConfigBuilder.produce(new RunTimeConfigBuilderBuildItem(SystemOnlySourcesConfigBuilder.class.getName()));
     }
 
+    /**
+     * Disable external configuration sources parsing for native executables since they are not supported see
+     * https://github.com/quarkusio/quarkus/issues/41994
+     */
+    @BuildStep(onlyIf = NativeOrNativeSourcesBuild.class)
+    void nativeNoSources(BuildProducer<StaticInitConfigBuilderBuildItem> staticInitConfigBuilder,
+            BuildProducer<RunTimeConfigBuilderBuildItem> runTimeConfigBuilder) {
+        runTimeConfigBuilder.produce(new RunTimeConfigBuilderBuildItem(SystemOnlySourcesConfigBuilder.class.getName()));
+    }
+
     private static class SystemOnlySources implements BooleanSupplier {
         ConfigBuildTimeConfig configBuildTimeConfig;