diff --git a/jooby/src/main/java/io/jooby/Jooby.java b/jooby/src/main/java/io/jooby/Jooby.java
index 3040d2ac47..77d758880d 100644
--- a/jooby/src/main/java/io/jooby/Jooby.java
+++ b/jooby/src/main/java/io/jooby/Jooby.java
@@ -131,9 +131,6 @@ public Jooby() {
     } else {
       copyState(owner, this);
     }
-    if (BOOT_SERVER != null) {
-      BOOT_SERVER.init(this);
-    }
   }
 
   @Override
@@ -1242,6 +1239,9 @@ public static void runApp(
       if (server.getOptions().defaults && appServerOptions != null) {
         server.setOptions(appServerOptions);
       }
+      for (var app : apps) {
+        server.init(app);
+      }
       targetServer.start(apps.toArray(new Jooby[0]));
     } catch (Throwable startupError) {
       try {
diff --git a/jooby/src/test/java/io/jooby/Issue3995.java b/jooby/src/test/java/io/jooby/Issue3995.java
new file mode 100644
index 0000000000..2c9e232bf2
--- /dev/null
+++ b/jooby/src/test/java/io/jooby/Issue3995.java
@@ -0,0 +1,54 @@
+/*
+ * Jooby https://jooby.io
+ * Apache License Version 2.0 https://jooby.io/LICENSE.txt
+ * Copyright 2014 Edgar Espina
+ */
+package io.jooby;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertSame;
+
+import org.junit.jupiter.api.Test;
+
+import io.jooby.output.OutputFactory;
+
+class Issue3995 {
+
+  private static class TestServer extends Server.Base {
+    @Override
+    public String getName() {
+      return "test-server";
+    }
+
+    @Override
+    public OutputFactory getOutputFactory() {
+      return OutputFactory.create();
+    }
+
+    @Override
+    public Server start(Jooby... application) {
+      return this;
+    }
+
+    @Override
+    public Server stop() {
+      return this;
+    }
+  }
+
+  @Test
+  void serverInitMustRunAfterFinalServerOptionsAreSet() {
+    var server = new TestServer();
+    var configured = new ServerOptions().setPort(3995);
+
+    Jooby app = Jooby.createApp(server, ExecutionMode.DEFAULT, () -> new Jooby() {});
+
+    server.setOptions(configured);
+    server.init(app);
+
+    var registryOptions = app.getServices().require(ServerOptions.class);
+    assertSame(configured, registryOptions);
+    assertEquals(3995, registryOptions.getPort());
+    assertEquals("test-server", registryOptions.getServer());
+  }
+}
diff --git a/jooby/src/test/java/io/jooby/JoobyRunnerTest.java b/jooby/src/test/java/io/jooby/JoobyRunnerTest.java
index 4f22789052..616fddb090 100644
--- a/jooby/src/test/java/io/jooby/JoobyRunnerTest.java
+++ b/jooby/src/test/java/io/jooby/JoobyRunnerTest.java
@@ -16,6 +16,7 @@
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.DisplayName;
 import org.junit.jupiter.api.Test;
+import org.mockito.InOrder;
 import org.mockito.MockedStatic;
 import org.mockito.Mockito;
 
@@ -93,8 +94,11 @@ void testRunApp_MultipleApps_MutedServer_DefaultsTrue() {
 
     // Verification
     // Defaults was true, so server.setOptions should be called with appOptions
-    verify(server).setOptions(appOptions);
-    verify(mutedServer).start(new Jooby[] {app1, app2});
+    InOrder inOrder = inOrder(server, mutedServer);
+    inOrder.verify(server).setOptions(appOptions);
+    inOrder.verify(server).init(app1);
+    inOrder.verify(server).init(app2);
+    inOrder.verify(mutedServer).start(new Jooby[] {app1, app2});
   }
 
   @Test
@@ -124,7 +128,9 @@ void testRunApp_SingleApp_NormalServer_DefaultsFalse() {
 
     // Verification
     verify(server, never()).setOptions(any()); // Because defaults == false
-    verify(server).start(new Jooby[] {app1});
+    InOrder inOrder = inOrder(server);
+    inOrder.verify(server).init(app1);
+    inOrder.verify(server).start(new Jooby[] {app1});
   }
 
   @DisplayName("Test Exception: StartupException thrown, stop throws ignored exception")
diff --git a/modules/jooby-test/src/main/java/io/jooby/test/JoobyExtension.java b/modules/jooby-test/src/main/java/io/jooby/test/JoobyExtension.java
index 1d5c4fb6d1..93624d75e3 100644
--- a/modules/jooby-test/src/main/java/io/jooby/test/JoobyExtension.java
+++ b/modules/jooby-test/src/main/java/io/jooby/test/JoobyExtension.java
@@ -77,6 +77,7 @@ private Jooby startApp(ExtensionContext context, JoobyTest metadata) throws Exce
       var defaultEnv = System.getProperty("application.env");
       System.setProperty("application.env", metadata.environment());
       app = Jooby.createApp(server, metadata.executionMode(), reflectionProvider(metadata.value()));
+      server.init(app);
       server.start(app);
       if (defaultEnv != null) {
         System.setProperty("application.env", defaultEnv);
@@ -85,6 +86,7 @@ private Jooby startApp(ExtensionContext context, JoobyTest metadata) throws Exce
       }
     } else {
       app = fromFactoryMethod(context, metadata, factoryMethod);
+      server.init(app);
       server.start(app);
     }
     ExtensionContext.Store store = getStore(context);
diff --git a/tests/src/test/java/io/jooby/junit/ServerTestRunner.java b/tests/src/test/java/io/jooby/junit/ServerTestRunner.java
index 256e2bd6e8..a92f7ab3b6 100644
--- a/tests/src/test/java/io/jooby/junit/ServerTestRunner.java
+++ b/tests/src/test/java/io/jooby/junit/ServerTestRunner.java
@@ -106,6 +106,7 @@ public void ready(SneakyThrows.Consumer2<WebClient, WebClient> onReady) {
       if (options.isSSLEnabled()) {
         options.setSecurePort(0);
       }
+      server.init(app);
       WebClient https = null;
       try {
         MutedServer.mute(server).start(app);