diff --git a/test-framework/junit5-internal/src/main/java/io/quarkus/test/QuarkusUnitTest.java b/test-framework/junit5-internal/src/main/java/io/quarkus/test/QuarkusUnitTest.java
index 3e0b9bb4d57470..62efc086836a43 100644
--- a/test-framework/junit5-internal/src/main/java/io/quarkus/test/QuarkusUnitTest.java
+++ b/test-framework/junit5-internal/src/main/java/io/quarkus/test/QuarkusUnitTest.java
@@ -6,6 +6,7 @@
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStream;
+import java.io.StringReader;
 import java.io.UncheckedIOException;
 import java.lang.reflect.Constructor;
 import java.lang.reflect.Field;
@@ -33,9 +34,13 @@
 import java.util.logging.Handler;
 import java.util.logging.LogManager;
 import java.util.logging.LogRecord;
+import java.util.stream.Collectors;
 
 import org.jboss.logmanager.Logger;
+import org.jboss.shrinkwrap.api.Node;
 import org.jboss.shrinkwrap.api.ShrinkWrap;
+import org.jboss.shrinkwrap.api.asset.Asset;
+import org.jboss.shrinkwrap.api.asset.StringAsset;
 import org.jboss.shrinkwrap.api.exporter.ExplodedExporter;
 import org.jboss.shrinkwrap.api.spec.JavaArchive;
 import org.junit.jupiter.api.extension.AfterAllCallback;
@@ -87,6 +92,7 @@ public class QuarkusUnitTest
 
     public static final String THE_BUILD_WAS_EXPECTED_TO_FAIL = "The build was expected to fail";
     private static final String APP_ROOT = "app-root";
+    private static final String APPLICATION_PROPERTIES = "application.properties";
 
     private static final Logger rootLogger;
     private Handler[] originalHandlers;
@@ -348,9 +354,40 @@ private void exportArchives(Path deploymentDir, Class<?> testClass) {
                 archive.addClass(c);
                 c = c.getSuperclass();
             }
+
+            Node applicationProperties = archive.get(APPLICATION_PROPERTIES);
             if (customApplicationProperties != null) {
-                archive.add(new PropertiesAsset(customApplicationProperties), "application.properties");
+                if (applicationProperties != null) {
+                    // We need to merge the existing "application.properties" asset and the overriden config properties
+                    Properties mergedProperties = new Properties();
+                    Asset asset = applicationProperties.getAsset();
+                    if (asset instanceof StringAsset strAsset) {
+                        mergedProperties.load(new StringReader(strAsset.getSource()));
+                    } else {
+                        try (InputStream in = asset.openStream()) {
+                            mergedProperties.load(in);
+                        }
+                    }
+                    // overrideConfigKey() takes precedence
+                    customApplicationProperties.forEach(mergedProperties::put);
+
+                    if (Boolean.parseBoolean(System.getProperty("quarkus.test.log-merged-properties"))) {
+                        System.out.println("Merged config properties:\n" + mergedProperties.entrySet().stream()
+                                .map(e -> e.getKey() + "=" + e.getValue()).collect(Collectors.joining("\n")));
+                    } else {
+                        System.out.println(
+                                "NOTE: overrideConfigKey() and application.properties were merged; use quarkus.test.log-merged-properties=true to list the specific values");
+                    }
+
+                    // MemoryMapArchiveBase#addAsset(ArchivePath,Asset) does not overwrite the existing node correctly
+                    // https://github.com/shrinkwrap/shrinkwrap/issues/179
+                    archive.delete(APPLICATION_PROPERTIES);
+                    archive.add(new PropertiesAsset(mergedProperties), APPLICATION_PROPERTIES);
+                } else {
+                    archive.add(new PropertiesAsset(customApplicationProperties), APPLICATION_PROPERTIES);
+                }
             }
+
             archive.as(ExplodedExporter.class).exportExplodedInto(deploymentDir.resolve(APP_ROOT).toFile());
 
             for (JavaArchive dependency : additionalDependencies) {