diff --git a/crates/ui-egui/src/lib.rs b/crates/ui-egui/src/lib.rs
index 92eba0fb0..00af44aa7 100644
--- a/crates/ui-egui/src/lib.rs
+++ b/crates/ui-egui/src/lib.rs
@@ -427,6 +427,7 @@ impl EffectcraftApp {
         self.ui.theme = theme::ThemeKind::from_name(p.appearance.resolved_theme(system)).unwrap_or_default();
         self.tokens = Tokens::from_prefs(p, self.ui.theme);
         theme::apply_visuals(ctx, &self.tokens);
+        ctx.set_theme(theme::theme_preference(&p.appearance.appearance_mode, self.ui.theme.is_light()));
         let tips = p.general.show_tool_tips;
         ctx.all_styles_mut(|s| s.interaction.tooltip_delay = if tips { 0.5 } else { f32::INFINITY });
         // Settings ▸ Appearance ▸ UI Scale (#284). egui's own Ctrl+= / Ctrl+- / Ctrl+0 zoom stays
@@ -1891,6 +1892,35 @@ mod appearance_tests {
         assert_eq!(app.ui.theme, ThemeKind::Dark);
     }
 
+    /// Sync with System leaves egui's theme preference at System, so egui never gives the native
+    /// window an appearance of its own (on macOS that stops system appearance changes reaching
+    /// the app, #642); egui's light and dark styles both carry the resolved theme. Fixed modes
+    /// pin the window to their family.
+    #[test]
+    fn auto_mode_leaves_the_native_window_following_the_system() {
+        let ctx = egui::Context::default();
+        let mut app = app();
+        app.hooks.system_theme = Some(Box::new(|_| Some(egui::Theme::Light)));
+        app.set_pref("appearance.appearanceMode", json!("auto")).unwrap();
+        app.apply_prefs(&ctx);
+        assert_eq!(app.ui.theme, ThemeKind::Light);
+        assert_eq!(ctx.options(|o| o.theme_preference), egui::ThemePreference::System);
+        for theme in [egui::Theme::Light, egui::Theme::Dark] {
+            assert_eq!(ctx.style_of(theme).visuals.panel_fill, app.tokens.panel_bg, "{theme:?}");
+        }
+        // egui asks the window to follow the system, never to take Light or Dark.
+        let mut out = ctx.run_ui(egui::RawInput::default(), |_| {});
+        out.textures_delta.clear();
+        let cmds = out.viewport_output.values().flat_map(|v| v.commands.iter()).collect::<Vec<_>>();
+        assert!(!cmds.iter().any(|c| matches!(c, egui::ViewportCommand::SetTheme(t) if t != &egui::SystemTheme::SystemDefault)), "{cmds:?}");
+        for (mode, pref) in [("light", egui::ThemePreference::Light), ("dark", egui::ThemePreference::Dark)] {
+            app.set_pref("appearance.appearanceMode", json!(mode)).unwrap();
+            app.apply_prefs(&ctx);
+            assert_eq!(ctx.options(|o| o.theme_preference), pref, "{mode}");
+            assert_eq!(ctx.global_style().visuals.panel_fill, app.tokens.panel_bg, "{mode}");
+        }
+    }
+
     /// Picking a theme (`view.theme.*`, `ui.set {theme}`) fixes the mode to its family.
     #[test]
     fn picking_a_theme_fixes_its_mode() {
diff --git a/crates/ui-egui/src/theme.rs b/crates/ui-egui/src/theme.rs
index 928dca9b4..febd19918 100644
--- a/crates/ui-egui/src/theme.rs
+++ b/crates/ui-egui/src/theme.rs
@@ -405,11 +405,20 @@ fn is_chinese(language: &str) -> bool {
     matches!(language, "zh-hans" | "zh-hant")
 }
 
+/// egui's theme preference for an appearance mode showing a `light` (or dark) theme. Sync with
+/// System leaves it at System: a concrete preference makes egui set the native window's
+/// appearance, and on macOS a window with its own appearance no longer hears when the system's
+/// changes (#642). A fixed Light or Dark mode pins the window to match.
+pub fn theme_preference(appearance_mode: &str, light: bool) -> egui::ThemePreference {
+    match appearance_mode {
+        "auto" => egui::ThemePreference::System,
+        _ if light => egui::ThemePreference::Light,
+        _ => egui::ThemePreference::Dark,
+    }
+}
+
 pub fn apply_visuals(ctx: &egui::Context, t: &Tokens) {
     let light = t.kind.is_light();
-    // egui keeps one style per light/dark theme and by default picks it by the system appearance;
-    // pin it to ours so a fixed Dark or Light mode isn't swapped for egui's defaults.
-    ctx.set_theme(if light { egui::ThemePreference::Light } else { egui::ThemePreference::Dark });
     let mut v = if light { Visuals::light() } else { Visuals::dark() };
     v.panel_fill = t.panel_bg;
     v.window_fill = t.panel_bg;
@@ -444,8 +453,10 @@ pub fn apply_visuals(ctx: &egui::Context, t: &Tokens) {
     v.widgets.active.fg_stroke = Stroke::new(1.0, t.tab_text_active);
     v.widgets.open.bg_fill = t.hover;
     v.widgets.open.weak_bg_fill = t.hover;
-    ctx.set_visuals(v);
-    ctx.global_style_mut(|s| {
+    // egui keeps one style per light/dark theme and picks it by its theme preference (see
+    // [`theme_preference`]); both get ours, so whichever it picks, egui's defaults never show.
+    ctx.all_styles_mut(|s| {
+        s.visuals = v.clone();
         s.spacing.item_spacing = egui::vec2(6.0, 4.0);
         s.spacing.button_padding = egui::vec2(8.0, 3.0);
         s.spacing.interact_size.y = 22.0;