diff --git a/core/deployment/src/main/java/io/quarkus/deployment/ForkJoinPoolProcessor.java b/core/deployment/src/main/java/io/quarkus/deployment/ForkJoinPoolProcessor.java
new file mode 100644
index 00000000000000..e98be4904efa01
--- /dev/null
+++ b/core/deployment/src/main/java/io/quarkus/deployment/ForkJoinPoolProcessor.java
@@ -0,0 +1,13 @@
+package io.quarkus.deployment;
+
+import io.quarkus.deployment.annotations.BuildStep;
+import io.quarkus.deployment.builditem.SystemPropertyBuildItem;
+
+public final class ForkJoinPoolProcessor {
+
+    @BuildStep
+    SystemPropertyBuildItem setProperty() {
+        return new SystemPropertyBuildItem("java.util.concurrent.ForkJoinPool.common.threadFactory",
+                "io.quarkus.bootstrap.forkjoin.QuarkusForkJoinWorkerThreadFactory");
+    }
+}
diff --git a/core/deployment/src/main/java/io/quarkus/deployment/jbang/JBangAugmentorImpl.java b/core/deployment/src/main/java/io/quarkus/deployment/jbang/JBangAugmentorImpl.java
index b49d007a01c752..db6a105b1b336f 100644
--- a/core/deployment/src/main/java/io/quarkus/deployment/jbang/JBangAugmentorImpl.java
+++ b/core/deployment/src/main/java/io/quarkus/deployment/jbang/JBangAugmentorImpl.java
@@ -124,6 +124,8 @@ public void accept(BuildChainBuilder builder) {
             resultMap.put("files", result);
             final List<String> javaargs = new ArrayList<>();
             javaargs.add("-Djava.util.logging.manager=org.jboss.logmanager.LogManager");
+            javaargs.add(
+                    "-Djava.util.concurrent.ForkJoinPool.common.threadFactory=io.quarkus.bootstrap.forkjoin.QuarkusForkJoinWorkerThreadFactory");
             resultMap.put("java-args", javaargs);
             resultMap.put("main-class", buildResult.consume(MainClassBuildItem.class).getClassName());
             if (nativeRequested) {
diff --git a/core/runtime/src/main/java/io/quarkus/runtime/Quarkus.java b/core/runtime/src/main/java/io/quarkus/runtime/Quarkus.java
index e6ecf8b5f4d11e..5b92c73344abef 100644
--- a/core/runtime/src/main/java/io/quarkus/runtime/Quarkus.java
+++ b/core/runtime/src/main/java/io/quarkus/runtime/Quarkus.java
@@ -5,7 +5,6 @@
 import java.util.function.BiConsumer;
 
 import org.jboss.logging.Logger;
-import org.jboss.logmanager.LogManager;
 
 import io.quarkus.launcher.QuarkusLauncher;
 
@@ -57,7 +56,9 @@ public static void run(Class<? extends QuarkusApplication> quarkusApplication, S
     public static void run(Class<? extends QuarkusApplication> quarkusApplication, BiConsumer<Integer, Throwable> exitHandler,
             String... args) {
         try {
-            System.setProperty("java.util.logging.manager", LogManager.class.getName());
+            System.setProperty("java.util.logging.manager", "org.jboss.logmanager.LogManager");
+            System.setProperty("java.util.concurrent.ForkJoinPool.common.threadFactory",
+                    "io.quarkus.bootstrap.forkjoin.QuarkusForkJoinWorkerThreadFactory");
             //production and common dev mode path
             //we already have an application, run it directly
             Class<? extends Application> appClass = (Class<? extends Application>) Class.forName(Application.APP_CLASS_NAME,
diff --git a/independent-projects/bootstrap/runner/src/main/java/io/quarkus/bootstrap/forkjoin/QuarkusForkJoinWorkerThread.java b/independent-projects/bootstrap/runner/src/main/java/io/quarkus/bootstrap/forkjoin/QuarkusForkJoinWorkerThread.java
new file mode 100644
index 00000000000000..9e00f5a06bcda1
--- /dev/null
+++ b/independent-projects/bootstrap/runner/src/main/java/io/quarkus/bootstrap/forkjoin/QuarkusForkJoinWorkerThread.java
@@ -0,0 +1,37 @@
+package io.quarkus.bootstrap.forkjoin;
+
+import io.quarkus.bootstrap.runner.RunnerClassLoader;
+import java.util.concurrent.ForkJoinPool;
+import java.util.concurrent.ForkJoinWorkerThread;
+
+public class QuarkusForkJoinWorkerThread extends ForkJoinWorkerThread {
+
+    private static volatile ClassLoader qClassloader;
+
+    protected QuarkusForkJoinWorkerThread(ForkJoinPool pool) {
+        super(pool);
+    }
+
+    public static synchronized void setQuarkusAppClassloader(RunnerClassLoader runnerClassLoader) {
+        if (qClassloader != null) {
+            throw new IllegalStateException("Attempting to set the Quarkus root classloader while it was already set");
+        }
+        if (runnerClassLoader == null) {
+            throw new IllegalStateException("Attempting to set the Quarkus root classloader to null");
+        }
+        qClassloader = runnerClassLoader;
+    }
+
+    protected void onStart() {
+        super.onStart();
+        if (qClassloader == null) {
+            throw new IllegalStateException(
+                    "Fork Join pool initialization has been triggered before the application classloader has been initialized. "
+                            +
+                            "Use this stacktrace to figure out what triggered it, and avoid using the Fork Join pool this early during the boot process.");
+        } else {
+            super.setContextClassLoader(qClassloader);
+        }
+    }
+
+}
diff --git a/independent-projects/bootstrap/runner/src/main/java/io/quarkus/bootstrap/forkjoin/QuarkusForkJoinWorkerThreadFactory.java b/independent-projects/bootstrap/runner/src/main/java/io/quarkus/bootstrap/forkjoin/QuarkusForkJoinWorkerThreadFactory.java
new file mode 100644
index 00000000000000..67f7d8344fff8b
--- /dev/null
+++ b/independent-projects/bootstrap/runner/src/main/java/io/quarkus/bootstrap/forkjoin/QuarkusForkJoinWorkerThreadFactory.java
@@ -0,0 +1,23 @@
+package io.quarkus.bootstrap.forkjoin;
+
+import java.util.concurrent.ForkJoinPool;
+import java.util.concurrent.ForkJoinWorkerThread;
+
+/**
+ * This implementation of JDK's ForkJoinPool.ForkJoinWorkerThreadFactory
+ * needs to be enabled by setting system property {@code java.util.concurrent.ForkJoinPool.common.threadFactory}
+ * to this class name, so to allow Quarkus to set the contextual classloader to the correct
+ * runtime classloader for each thread being started by the common pool.
+ * Otherwise the system classloader will be set, which is unable to load all application resources.
+ */
+public final class QuarkusForkJoinWorkerThreadFactory implements ForkJoinPool.ForkJoinWorkerThreadFactory {
+
+    public QuarkusForkJoinWorkerThreadFactory() {
+    }
+
+    @Override
+    public ForkJoinWorkerThread newThread(ForkJoinPool pool) {
+        return new QuarkusForkJoinWorkerThread(pool);
+    }
+
+}
diff --git a/independent-projects/bootstrap/runner/src/main/java/io/quarkus/bootstrap/runner/QuarkusEntryPoint.java b/independent-projects/bootstrap/runner/src/main/java/io/quarkus/bootstrap/runner/QuarkusEntryPoint.java
index 2ae1c385cfe5a5..6b543df1886483 100644
--- a/independent-projects/bootstrap/runner/src/main/java/io/quarkus/bootstrap/runner/QuarkusEntryPoint.java
+++ b/independent-projects/bootstrap/runner/src/main/java/io/quarkus/bootstrap/runner/QuarkusEntryPoint.java
@@ -1,5 +1,6 @@
 package io.quarkus.bootstrap.runner;
 
+import io.quarkus.bootstrap.forkjoin.QuarkusForkJoinWorkerThread;
 import java.io.BufferedInputStream;
 import java.io.File;
 import java.io.IOException;
@@ -21,6 +22,8 @@ public class QuarkusEntryPoint {
 
     public static void main(String... args) throws Throwable {
         System.setProperty("java.util.logging.manager", org.jboss.logmanager.LogManager.class.getName());
+        System.setProperty("java.util.concurrent.ForkJoinPool.common.threadFactory",
+                "io.quarkus.bootstrap.forkjoin.QuarkusForkJoinWorkerThreadFactory");
         Timing.staticInitStarted(false);
         doRun(args);
     }
@@ -44,6 +47,7 @@ private static void doRun(Object args) throws IOException, ClassNotFoundExceptio
             }
             try {
                 Thread.currentThread().setContextClassLoader(app.getRunnerClassLoader());
+                QuarkusForkJoinWorkerThread.setQuarkusAppClassloader(app.getRunnerClassLoader());
                 Class<?> mainClass = app.getRunnerClassLoader().loadClass(app.getMainClass());
                 mainClass.getMethod("main", String[].class).invoke(null, args);
             } finally {