diff --git a/.changes/core-navigation-handler.md b/.changes/core-navigation-handler.md
new file mode 100644
index 000000000..ea91d5e04
--- /dev/null
+++ b/.changes/core-navigation-handler.md
@@ -0,0 +1,5 @@
+---
+'tauri': 'patch'
+---
+
+Fix `WindowBuilder::on_navigation` handler not registered properly.
diff --git a/core/tauri-runtime/src/window.rs b/core/tauri-runtime/src/window.rs
index af15dac05..8364c36b1 100644
--- a/core/tauri-runtime/src/window.rs
+++ b/core/tauri-runtime/src/window.rs
@@ -24,6 +24,8 @@ use std::{
 type UriSchemeProtocol =
   dyn Fn(&HttpRequest) -> Result<HttpResponse, Box<dyn std::error::Error>> + Send + Sync + 'static;
 
+type WebResourceRequestHandler = dyn Fn(&HttpRequest, &mut HttpResponse) + Send + Sync;
+
 /// UI scaling utilities.
 pub mod dpi;
 
@@ -234,6 +236,8 @@ pub struct PendingWindow<T: UserEvent, R: Runtime<T>> {
   /// A handler to decide if incoming url is allowed to navigate.
   pub navigation_handler: Option<Box<dyn Fn(Url) -> bool + Send>>,
 
+  pub web_resource_request_handler: Option<Box<WebResourceRequestHandler>>,
+
   /// The current webview URL.
   pub current_url: Arc<Mutex<Url>>,
 }
@@ -275,6 +279,7 @@ impl<T: UserEvent, R: Runtime<T>> PendingWindow<T, R> {
         menu_ids: Arc::new(Mutex::new(menu_ids)),
         js_event_listeners: Default::default(),
         navigation_handler: Default::default(),
+        web_resource_request_handler: Default::default(),
         current_url: Arc::new(Mutex::new("tauri://localhost".parse().unwrap())),
       })
     }
@@ -305,6 +310,7 @@ impl<T: UserEvent, R: Runtime<T>> PendingWindow<T, R> {
         menu_ids: Arc::new(Mutex::new(menu_ids)),
         js_event_listeners: Default::default(),
         navigation_handler: Default::default(),
+        web_resource_request_handler: Default::default(),
         current_url: Arc::new(Mutex::new("tauri://localhost".parse().unwrap())),
       })
     }
diff --git a/core/tauri/src/app.rs b/core/tauri/src/app.rs
index 544977324..f2db2494c 100644
--- a/core/tauri/src/app.rs
+++ b/core/tauri/src/app.rs
@@ -1705,10 +1705,9 @@ impl<R: Runtime> Builder<R> {
       .collect::<Vec<_>>();
 
     for pending in self.pending_windows {
-      let pending =
-        app
-          .manager
-          .prepare_window(app.handle.clone(), pending, &window_labels, None)?;
+      let pending = app
+        .manager
+        .prepare_window(app.handle.clone(), pending, &window_labels)?;
       let detached = app.runtime.as_ref().unwrap().create_window(pending)?;
       let _window = app.manager.attach_window(app.handle(), detached);
     }
diff --git a/core/tauri/src/manager.rs b/core/tauri/src/manager.rs
index d613251ac..b7d8a2539 100644
--- a/core/tauri/src/manager.rs
+++ b/core/tauri/src/manager.rs
@@ -25,6 +25,7 @@ use tauri_utils::{
   html::{SCRIPT_NONCE_TOKEN, STYLE_NONCE_TOKEN},
 };
 
+use crate::app::{GlobalMenuEventListener, WindowMenuEvent};
 use crate::hooks::IpcJavascript;
 #[cfg(feature = "isolation")]
 use crate::hooks::IsolationJavascript;
@@ -50,10 +51,6 @@ use crate::{
   Context, EventLoopMessage, Icon, Invoke, Manager, Pattern, Runtime, Scopes, StateManager, Window,
   WindowEvent,
 };
-use crate::{
-  app::{GlobalMenuEventListener, WindowMenuEvent},
-  window::WebResourceRequestHandler,
-};
 
 #[cfg(any(target_os = "linux", target_os = "windows"))]
 use crate::api::path::{resolve_path, BaseDirectory};
@@ -401,7 +398,6 @@ impl<R: Runtime> WindowManager<R> {
     label: &str,
     window_labels: &[String],
     app_handle: AppHandle<R>,
-    web_resource_request_handler: Option<Box<WebResourceRequestHandler>>,
   ) -> crate::Result<PendingWindow<EventLoopMessage, R>> {
     let is_init_global = self.inner.config.build.with_global_tauri;
     let plugin_init = self
@@ -492,6 +488,7 @@ impl<R: Runtime> WindowManager<R> {
       };
 
     if !registered_scheme_protocols.contains(&"tauri".into()) {
+      let web_resource_request_handler = pending.web_resource_request_handler.take();
       pending.register_uri_scheme_protocol(
         "tauri",
         self.prepare_uri_scheme_protocol(&window_origin, web_resource_request_handler),
@@ -1122,7 +1119,6 @@ impl<R: Runtime> WindowManager<R> {
     app_handle: AppHandle<R>,
     mut pending: PendingWindow<EventLoopMessage, R>,
     window_labels: &[String],
-    web_resource_request_handler: Option<Box<WebResourceRequestHandler>>,
   ) -> crate::Result<PendingWindow<EventLoopMessage, R>> {
     if self.windows_lock().contains_key(&pending.label) {
       return Err(crate::Error::WindowLabelAlreadyExists(pending.label));
@@ -1186,13 +1182,7 @@ impl<R: Runtime> WindowManager<R> {
     }
 
     let label = pending.label.clone();
-    pending = self.prepare_pending_window(
-      pending,
-      &label,
-      window_labels,
-      app_handle.clone(),
-      web_resource_request_handler,
-    )?;
+    pending = self.prepare_pending_window(pending, &label, window_labels, app_handle.clone())?;
     pending.ipc_handler = Some(self.prepare_ipc_handler(app_handle));
 
     // in `Windows`, we need to force a data_directory
diff --git a/core/tauri/src/window.rs b/core/tauri/src/window.rs
index b14b6d2cb..e8b4d11fa 100644
--- a/core/tauri/src/window.rs
+++ b/core/tauri/src/window.rs
@@ -310,19 +310,18 @@ impl<'a, R: Runtime> WindowBuilder<'a, R> {
 
   /// Creates a new webview window.
   pub fn build(mut self) -> crate::Result<Window<R>> {
-    let web_resource_request_handler = self.web_resource_request_handler.take();
-    let pending = PendingWindow::new(
+    let mut pending = PendingWindow::new(
       self.window_builder.clone(),
       self.webview_attributes.clone(),
       self.label.clone(),
     )?;
+    pending.navigation_handler = self.navigation_handler.take();
+    pending.web_resource_request_handler = self.web_resource_request_handler.take();
+
     let labels = self.manager.labels().into_iter().collect::<Vec<_>>();
-    let pending = self.manager.prepare_window(
-      self.app_handle.clone(),
-      pending,
-      &labels,
-      web_resource_request_handler,
-    )?;
+    let pending = self
+      .manager
+      .prepare_window(self.app_handle.clone(), pending, &labels)?;
 
     let window = match &mut self.runtime {
       RuntimeOrDispatch::Runtime(runtime) => runtime.create_window(pending),