diff --git a/test-framework/junit5/src/main/java/io/quarkus/test/junit/AbstractJvmQuarkusTestExtension.java b/test-framework/junit5/src/main/java/io/quarkus/test/junit/AbstractJvmQuarkusTestExtension.java
index a7bf610f10f44..9254f46e1d271 100644
--- a/test-framework/junit5/src/main/java/io/quarkus/test/junit/AbstractJvmQuarkusTestExtension.java
+++ b/test-framework/junit5/src/main/java/io/quarkus/test/junit/AbstractJvmQuarkusTestExtension.java
@@ -4,6 +4,7 @@
 import static io.quarkus.test.common.PathTestHelper.getAppClassLocationForTestLocation;
 import static io.quarkus.test.common.PathTestHelper.getTestClassesLocation;
 
+import java.io.FileOutputStream;
 import java.io.IOException;
 import java.lang.annotation.Annotation;
 import java.nio.file.Files;
@@ -15,6 +16,7 @@
 import java.util.HashMap;
 import java.util.Map;
 import java.util.Optional;
+import java.util.Properties;
 import java.util.function.Consumer;
 import java.util.stream.Collectors;
 
@@ -40,7 +42,6 @@
 import io.quarkus.runtime.LaunchMode;
 import io.quarkus.test.common.PathTestHelper;
 import io.quarkus.test.common.QuarkusTestResource;
-import io.quarkus.test.common.RestorableSystemProperties;
 import io.quarkus.test.common.TestClassIndexer;
 import io.quarkus.test.common.WithTestResource;
 
@@ -147,31 +148,59 @@ protected PrepareResult createAugmentor(ExtensionContext context, Class<? extend
 
         // clear the test.url system property as the value leaks into the run when using different profiles
         System.clearProperty("test.url");
-        Map<String, String> additional = new HashMap<>();
 
         QuarkusTestProfile profileInstance = null;
         if (profile != null) {
             profileInstance = profile.getConstructor().newInstance();
-            additional.putAll(profileInstance.getConfigOverrides());
+
+            Map<String, String> overrides = new HashMap<>(profileInstance.getConfigOverrides());
             if (!profileInstance.getEnabledAlternatives().isEmpty()) {
-                additional.put("quarkus.arc.selected-alternatives", profileInstance.getEnabledAlternatives().stream()
-                        .peek((c) -> {
-                            if (!c.isAnnotationPresent(Alternative.class)) {
-                                throw new RuntimeException(
-                                        "Enabled alternative " + c + " is not annotated with @Alternative");
-                            }
-                        })
-                        .map(Class::getName).collect(Collectors.joining(",")));
+                overrides.put("quarkus.arc.selected-alternatives",
+                        profileInstance.getEnabledAlternatives()
+                                .stream()
+                                .peek((c) -> {
+                                    if (!c.isAnnotationPresent(Alternative.class)) {
+                                        throw new RuntimeException(
+                                                "Enabled alternative " + c + " is not annotated with " +
+                                                        "@Alternative");
+                                    }
+                                })
+                                .map(Class::getName)
+                                .collect(Collectors.joining(",")));
             }
             if (profileInstance.disableApplicationLifecycleObservers()) {
-                additional.put("quarkus.arc.test.disable-application-lifecycle-observers", "true");
+                overrides.put("quarkus.arc.test.disable-application-lifecycle-observers", "true");
             }
             if (profileInstance.getConfigProfile() != null) {
-                additional.put(LaunchMode.TEST.getProfileKey(), profileInstance.getConfigProfile());
+                overrides.put(LaunchMode.TEST.getProfileKey(), profileInstance.getConfigProfile());
+            }
+
+            // Creates a temporary application.properties file for the test with a high ordinal (build and runtime)
+            Path tempDirectory = Files.createTempDirectory(testClassLocation, requiredTestClass.getSimpleName());
+            Path propertiesFile = tempDirectory.resolve("application.properties");
+            Files.createFile(propertiesFile);
+            Properties properties = new Properties();
+            // TODO - radcortez - This should be higher that system properties, but configuration like ports is being
+            // passed around using system properties, meaning that it cannot be overridden. We cannot use system
+            // properties to carry that information. See io.quarkus.vertx.http.runtime.PortSystemProperties
+            properties.put("config_ordinal", "399");
+            properties.putAll(overrides);
+            try (FileOutputStream outputStream = new FileOutputStream(propertiesFile.toFile())) {
+                properties.store(outputStream, "");
             }
-            //we just use system properties for now
-            //it's a lot simpler
-            shutdownTasks.add(RestorableSystemProperties.setProperties(additional)::close);
+            addToBuilderIfConditionMet.accept(tempDirectory);
+
+            shutdownTasks.add(new Runnable() {
+                @Override
+                public void run() {
+                    try {
+                        Files.deleteIfExists(propertiesFile);
+                        Files.deleteIfExists(tempDirectory);
+                    } catch (IOException e) {
+                        throw new RuntimeException(e);
+                    }
+                }
+            });
         }
 
         CuratedApplication curatedApplication;
diff --git a/test-framework/junit5/src/main/java/io/quarkus/test/junit/QuarkusMainTestExtension.java b/test-framework/junit5/src/main/java/io/quarkus/test/junit/QuarkusMainTestExtension.java
index d793d8e74b6c4..744e35bc67d0a 100644
--- a/test-framework/junit5/src/main/java/io/quarkus/test/junit/QuarkusMainTestExtension.java
+++ b/test-framework/junit5/src/main/java/io/quarkus/test/junit/QuarkusMainTestExtension.java
@@ -77,9 +77,8 @@ private void ensurePrepared(ExtensionContext extensionContext, Class<? extends Q
             prepareResult = null;
         }
         if (prepareResult == null) {
-            final LinkedBlockingDeque<Runnable> shutdownTasks = new LinkedBlockingDeque<>();
-            PrepareResult result = createAugmentor(extensionContext, profile, shutdownTasks);
-            prepareResult = result;
+            LinkedBlockingDeque<Runnable> shutdownTasks = new LinkedBlockingDeque<>();
+            prepareResult = createAugmentor(extensionContext, profile, shutdownTasks);
         }
     }
 
diff --git a/test-framework/junit5/src/main/java/io/quarkus/test/junit/QuarkusTestExtension.java b/test-framework/junit5/src/main/java/io/quarkus/test/junit/QuarkusTestExtension.java
index 0f881f19022ce..915f33f98eda1 100644
--- a/test-framework/junit5/src/main/java/io/quarkus/test/junit/QuarkusTestExtension.java
+++ b/test-framework/junit5/src/main/java/io/quarkus/test/junit/QuarkusTestExtension.java
@@ -205,12 +205,12 @@ public Thread newThread(Runnable r) {
         }
         hangTimeout = new DurationConverter().convert(time);
         hangTaskKey = hangDetectionExecutor.schedule(hangDetectionTask, hangTimeout.toMillis(), TimeUnit.MILLISECONDS);
-
         quarkusTestProfile = profile;
+
+        LinkedBlockingDeque<Runnable> shutdownTasks = new LinkedBlockingDeque<>();
         Class<?> requiredTestClass = context.getRequiredTestClass();
         Closeable testResourceManager = null;
         try {
-            final LinkedBlockingDeque<Runnable> shutdownTasks = new LinkedBlockingDeque<>();
             PrepareResult result = createAugmentor(context, profile, shutdownTasks);
             AugmentAction augmentAction = result.augmentAction;
             QuarkusTestProfile profileInstance = result.profileInstance;
@@ -298,8 +298,7 @@ public void close() throws IOException {
                     }
                 }
             };
-            ExtensionState state = new ExtensionState(testResourceManager, shutdownTask);
-            return state;
+            return new ExtensionState(testResourceManager, shutdownTask);
         } catch (Throwable e) {
             if (!InitialConfigurator.DELAYED_HANDLER.isActivated()) {
                 activateLogging();
@@ -315,6 +314,16 @@ public void close() throws IOException {
                 effectiveException.addSuppressed(determineEffectiveException(ex));
             }
 
+            while (!shutdownTasks.isEmpty()) {
+                shutdownTasks.pop().run();
+            }
+
+            try {
+                TestClassIndexer.removeIndex(requiredTestClass);
+            } catch (Exception ignored) {
+
+            }
+
             throw effectiveException;
         } finally {
             if (originalCl != null) {