diff --git a/cosmic-config/src/lib.rs b/cosmic-config/src/lib.rs
index 1a3ec66a..e408eac5 100644
--- a/cosmic-config/src/lib.rs
+++ b/cosmic-config/src/lib.rs
@@ -10,7 +10,6 @@ use std::{
     io::Write,
     path::{Path, PathBuf},
     sync::Mutex,
-    time::Duration,
 };
 
 #[cfg(feature = "subscription")]
diff --git a/src/app/cosmic.rs b/src/app/cosmic.rs
index 3a75871d..a2cdeb87 100644
--- a/src/app/cosmic.rs
+++ b/src/app/cosmic.rs
@@ -17,6 +17,8 @@ use iced::Application as IcedApplication;
 use iced::event::wayland;
 use iced::{Task, window};
 use iced_futures::event::listen_with;
+#[cfg(feature = "wayland")]
+use iced_winit::SurfaceIdWrapper;
 use palette::color_difference::EuclideanDistance;
 
 #[derive(Copy, Clone, Debug, Eq, PartialEq, Hash)]
@@ -84,7 +86,11 @@ pub struct Cosmic<App: Application> {
     #[cfg(feature = "wayland")]
     pub surface_views: HashMap<
         window::Id,
-        Box<dyn for<'a> Fn(&'a App) -> Element<'a, crate::Action<App::Message>>>,
+        (
+            Option<window::Id>,
+            SurfaceIdWrapper,
+            Box<dyn for<'a> Fn(&'a App) -> Element<'a, crate::Action<App::Message>>>,
+        ),
     >,
 }
 
@@ -449,7 +455,7 @@ where
     #[cfg(feature = "multi-window")]
     pub fn view(&self, id: window::Id) -> Element<crate::Action<T::Message>> {
         #[cfg(feature = "wayland")]
-        if let Some(v) = self.surface_views.get(&id) {
+        if let Some((_, _, v)) = self.surface_views.get(&id) {
             return v(&self.app);
         }
         if self
@@ -841,13 +847,45 @@ impl<T: Application> Cosmic<T> {
             }
 
             Action::Focus(f) => {
-                self.app.core_mut().focused_window = Some(f);
+                #[cfg(all(
+                    feature = "wayland",
+                    feature = "multi-window",
+                    feature = "surface-message"
+                ))]
+                if let Some((
+                    parent,
+                    SurfaceIdWrapper::Subsurface(_) | SurfaceIdWrapper::Popup(_),
+                    _,
+                )) = self.surface_views.get(&f)
+                {
+                    // If the parent is already focused, push the new focus
+                    // to the end of the focus chain.
+                    if parent.is_some_and(|p| self.app.core().focused_window.last() == Some(&p)) {
+                        self.app.core_mut().focused_window.push(f);
+                        return iced::Task::none();
+                    } else {
+                        // set the whole parent chain to the focus chain
+                        let mut parent_chain = vec![f];
+                        let mut cur = *parent;
+                        while let Some(p) = cur {
+                            parent_chain.push(p);
+                            cur = self
+                                .surface_views
+                                .get(&p)
+                                .and_then(|(parent, _, _)| *parent);
+                        }
+                        parent_chain.reverse();
+                        self.app.core_mut().focused_window = parent_chain;
+                        return iced::Task::none();
+                    }
+                }
+                self.app.core_mut().focused_window = vec![f];
             }
 
             Action::Unfocus(id) => {
                 let core = self.app.core_mut();
-                if core.focused_window.as_ref().is_some_and(|cur| *cur == id) {
-                    core.focused_window = None;
+                if core.focused_window().as_ref().is_some_and(|cur| *cur == id) {
+                    core.focused_window.pop();
                 }
             }
             #[cfg(feature = "applet")]
@@ -886,7 +924,14 @@ impl<App: Application> Cosmic<App> {
     ) -> Task<crate::Action<App::Message>> {
         use iced_winit::commands::subsurface::get_subsurface;
 
-        self.surface_views.insert(settings.id, view);
+        self.surface_views.insert(
+            settings.id,
+            (
+                Some(settings.parent),
+                SurfaceIdWrapper::Subsurface(settings.id),
+                view,
+            ),
+        );
         get_subsurface(settings)
     }
 
@@ -901,7 +946,14 @@ impl<App: Application> Cosmic<App> {
     ) -> Task<crate::Action<App::Message>> {
         use iced_winit::commands::popup::get_popup;
 
-        self.surface_views.insert(settings.id, view);
+        self.surface_views.insert(
+            settings.id,
+            (
+                Some(settings.parent),
+                SurfaceIdWrapper::Popup(settings.id),
+                view,
+            ),
+        );
         get_popup(settings)
     }
 }
diff --git a/src/app/mod.rs b/src/app/mod.rs
index 890a3429..35b55f02 100644
--- a/src/app/mod.rs
+++ b/src/app/mod.rs
@@ -548,8 +548,9 @@ impl<App: Application> ApplicationExt for App {
         let show_context = core.window.show_context;
         let nav_bar_active = core.nav_bar_active();
         let focused = core
-            .focused_window()
-            .is_some_and(|i| Some(i) == self.core().main_window_id());
+            .focus_chain()
+            .iter()
+            .any(|i| Some(*i) == self.core().main_window_id());
 
         let border_padding = if sharp_corners { 8 } else { 7 };
 
diff --git a/src/core.rs b/src/core.rs
index 744b33b7..4b9811ec 100644
--- a/src/core.rs
+++ b/src/core.rs
@@ -64,7 +64,7 @@ pub struct Core {
     scale_factor: f32,
 
     /// Window focus state
-    pub(super) focused_window: Option<window::Id>,
+    pub(super) focused_window: Vec<window::Id>,
 
     pub(super) theme_sub_counter: u64,
     /// Last known system theme
@@ -141,7 +141,7 @@ impl Default for Core {
                 height: 0.,
                 width: 0.,
             },
-            focused_window: None,
+            focused_window: Vec::new(),
             #[cfg(feature = "applet")]
             applet: crate::applet::Context::default(),
             #[cfg(feature = "single-instance")]
@@ -384,8 +384,15 @@ impl Core {
     /// Get the current focused window if it exists
     #[must_use]
     #[inline]
-    pub const fn focused_window(&self) -> Option<window::Id> {
-        self.focused_window
+    pub fn focused_window(&self) -> Option<window::Id> {
+        self.focused_window.last().copied()
+    }
+
+    /// Get the current focus chain of windows
+    #[must_use]
+    #[inline]
+    pub fn focus_chain(&self) -> &[window::Id] {
+        &self.focused_window
     }
 
     /// Whether the application should use a dark theme, according to the system