diff --git a/src/bubble.rs b/src/bubble.rs
index b2b7d46..68e280f 100644
--- a/src/bubble.rs
+++ b/src/bubble.rs
@@ -351,6 +351,8 @@ pub fn create(app: &AppHandle, provider: ProviderId) -> tauri::Result<()> {
         set_position(&window, placement.pos);
     }
     set_size(&window, placement.size);
+    // Windows applies it on the main thread, in `prepare_native`.
+    #[cfg(not(windows))]
     if click_through {
         set_ignore_cursor(&window, true);
     }
@@ -363,7 +365,7 @@ pub fn create(app: &AppHandle, provider: ProviderId) -> tauri::Result<()> {
         placement.dpi
     );
 
-    prepare_native(app, &window, provider);
+    prepare_native(app, &window, provider, click_through);
     #[cfg(target_os = "linux")]
     if let Some(is_dark) = platform::linux::portal_prefers_dark() {
         runtime.set_dark(is_dark);
@@ -399,13 +401,21 @@ pub fn create(app: &AppHandle, provider: ProviderId) -> tauri::Result<()> {
 /// move-end, setting-change and display-change messages. Both must run on
 /// the window's own (main) thread before the first show.
 #[cfg(windows)]
-fn prepare_native(app: &AppHandle, window: &WebviewWindow, provider: ProviderId) {
+fn prepare_native(
+    app: &AppHandle,
+    window: &WebviewWindow,
+    provider: ProviderId,
+    click_through: bool,
+) {
     let window = window.clone();
     let hook_app = app.clone();
     let queued = app.run_on_main_thread(move || {
         if let Err(err) = platform::windows::apply_no_activate(&window) {
             log::warn!("{} may take focus: {err}", window.label());
         }
+        if click_through {
+            set_ignore_cursor(&window, true);
+        }
         let hooked = platform::windows::install_bubble_hook(&window, move |event| {
             on_hook_event(&hook_app, provider, event);
         });
@@ -419,7 +429,13 @@ fn prepare_native(app: &AppHandle, window: &WebviewWindow, provider: ProviderId)
 }
 
 #[cfg(not(windows))]
-fn prepare_native(_app: &AppHandle, _window: &WebviewWindow, _provider: ProviderId) {}
+fn prepare_native(
+    _app: &AppHandle,
+    _window: &WebviewWindow,
+    _provider: ProviderId,
+    _click_through: bool,
+) {
+}
 
 #[cfg(windows)]
 fn on_hook_event(app: &AppHandle, provider: ProviderId, event: platform::windows::BubbleHookEvent) {
@@ -565,8 +581,18 @@ pub fn set_click_through(app: &AppHandle, ignore: bool) {
     }
 }
 
+/// On Windows the style bits are set directly: tao's
+/// `set_ignore_cursor_events` re-applies all its window flags, and since
+/// bubbles are shown through [`show`], not tao, it believes them hidden and
+/// hides them, also dropping their no-activate and tool-window styles.
 fn set_ignore_cursor(window: &WebviewWindow, ignore: bool) {
-    if let Err(err) = window.set_ignore_cursor_events(ignore) {
+    #[cfg(windows)]
+    let result = platform::windows::set_click_through(window, ignore).map_err(|e| e.to_string());
+    #[cfg(not(windows))]
+    let result = window
+        .set_ignore_cursor_events(ignore)
+        .map_err(|e| e.to_string());
+    if let Err(err) = result {
         log::warn!("{} click-through not set: {err}", window.label());
     }
 }
diff --git a/src/platform/windows.rs b/src/platform/windows.rs
index f848248..064b399 100644
--- a/src/platform/windows.rs
+++ b/src/platform/windows.rs
@@ -31,8 +31,8 @@ use windows::Win32::UI::WindowsAndMessaging::{
     SetWindowLongPtrW, SetWindowPos, ShowWindow, GWL_EXSTYLE, GWL_STYLE, GW_HWNDPREV, HWND_TOPMOST,
     MA_NOACTIVATE, MB_ICONERROR, MB_OK, MB_SETFOREGROUND, SWP_FRAMECHANGED, SWP_NOACTIVATE,
     SWP_NOMOVE, SWP_NOSIZE, SWP_NOZORDER, SW_HIDE, SW_SHOWNOACTIVATE, WM_DISPLAYCHANGE,
-    WM_EXITSIZEMOVE, WM_MOUSEACTIVATE, WM_NCDESTROY, WM_SETTINGCHANGE, WS_EX_NOACTIVATE,
-    WS_EX_TOOLWINDOW, WS_EX_TOPMOST,
+    WM_EXITSIZEMOVE, WM_MOUSEACTIVATE, WM_NCDESTROY, WM_SETTINGCHANGE, WS_EX_LAYERED,
+    WS_EX_NOACTIVATE, WS_EX_TOOLWINDOW, WS_EX_TOPMOST, WS_EX_TRANSPARENT,
 };
 
 use crate::core::geom::{self, Edge, Rect};
@@ -203,19 +203,34 @@ pub fn apply_toolwindow(window: &tauri::WebviewWindow) -> io::Result<()> {
     add_ex_style(window, WS_EX_TOOLWINDOW.0)
 }
 
+/// Let mouse input pass through a bubble to the windows below, or take it
+/// again. These are the bits tao's `set_ignore_cursor_events` sets, without
+/// its re-applying every window flag, which hides a bubble shown through
+/// [`show_no_activate`]. Run it on the window's own (main) thread.
+pub fn set_click_through(window: &tauri::WebviewWindow, ignore: bool) -> io::Result<()> {
+    set_ex_style(window, (WS_EX_TRANSPARENT | WS_EX_LAYERED).0, ignore)
+}
+
 /// OR `bits` into a window's extended style and apply the frame change.
 fn add_ex_style(window: &tauri::WebviewWindow, bits: u32) -> io::Result<()> {
+    set_ex_style(window, bits, true)
+}
+
+/// Set or clear `bits` in a window's extended style and apply the frame
+/// change.
+fn set_ex_style(window: &tauri::WebviewWindow, bits: u32, on: bool) -> io::Result<()> {
     let hwnd = hwnd_of(window)?;
-    let wanted = bits as isize;
+    let bits = bits as isize;
     // SAFETY: `hwnd` is a live top-level window of this process.
     let current = unsafe { GetWindowLongPtrW(hwnd, GWL_EXSTYLE) };
-    if current & wanted == wanted {
+    let wanted = if on { current | bits } else { current & !bits };
+    if wanted == current {
         return Ok(());
     }
     // SAFETY: as above. A zero return is only an error when the last error
     // is set, so it is cleared first.
     unsafe { SetLastError(WIN32_ERROR(0)) };
-    let previous = unsafe { SetWindowLongPtrW(hwnd, GWL_EXSTYLE, current | wanted) };
+    let previous = unsafe { SetWindowLongPtrW(hwnd, GWL_EXSTYLE, wanted) };
     if previous == 0 {
         let err = io::Error::last_os_error();
         if err.raw_os_error().unwrap_or(0) != 0 {