diff --git a/core/deployment/src/main/java/io/quarkus/deployment/steps/MainClassBuildStep.java b/core/deployment/src/main/java/io/quarkus/deployment/steps/MainClassBuildStep.java
index 9b5a17a380853..94edce4e414e9 100644
--- a/core/deployment/src/main/java/io/quarkus/deployment/steps/MainClassBuildStep.java
+++ b/core/deployment/src/main/java/io/quarkus/deployment/steps/MainClassBuildStep.java
@@ -240,8 +240,9 @@ void build(List<StaticBytecodeRecorderBuildItem> staticInitTasks,
             createAppCDS.returnValue(null);
         }
 
-        // very first thing is to set system props (for run time, which use substitutions for a different
-        // storage from build-time)
+        // Make sure we set properties in doStartup as well. This is necessary because setting them in the static-init
+        // sets them at build-time, on the host JVM, while SVM has substitutions for System. get/ setProperty at
+        // run-time which will never see those properties unless we also set them at run-time.
         for (SystemPropertyBuildItem i : properties) {
             mv.invokeStaticMethod(ofMethod(System.class, "setProperty", String.class, String.class, String.class),
                     mv.load(i.getKey()), mv.load(i.getValue()));