diff --git a/changes/fix-hyprland-settings-window-z-order.md b/changes/fix-hyprland-settings-window-z-order.md
new file mode 100644
index 00000000..972801f6
--- /dev/null
+++ b/changes/fix-hyprland-settings-window-z-order.md
@@ -0,0 +1,4 @@
+type: fixed
+area: desktop
+
+- Fixed Hyprland settings windows opening behind the subtitle overlay by promoting SubMiner and Yomitan settings above the overlay without hiding subtitles.
diff --git a/changes/fix-linux-app-command-detach.md b/changes/fix-linux-app-command-detach.md
new file mode 100644
index 00000000..d0920680
--- /dev/null
+++ b/changes/fix-linux-app-command-detach.md
@@ -0,0 +1,4 @@
+type: fixed
+area: launcher
+
+- Fixed `subminer app` on Linux so launching the tray app returns control to the terminal immediately instead of waiting for the tray process to exit.
diff --git a/launcher/commands/app-command.ts b/launcher/commands/app-command.ts
index 3073aa8f..adc58a5e 100644
--- a/launcher/commands/app-command.ts
+++ b/launcher/commands/app-command.ts
@@ -6,7 +6,6 @@ import {
 import type { LauncherCommandContext } from './context.js';
 
 type AppCommandDeps = {
-  platform: () => NodeJS.Platform;
   runAppCommandWithInherit: (appPath: string, appArgs: string[]) => void;
   launchAppBackgroundDetached: (
     appPath: string,
@@ -15,7 +14,6 @@ type AppCommandDeps = {
 };
 
 const defaultAppCommandDeps: AppCommandDeps = {
-  platform: () => process.platform,
   runAppCommandWithInherit,
   launchAppBackgroundDetached,
 };
@@ -35,7 +33,7 @@ export function runAppPassthroughCommand(
   if (!args.appPassthrough) {
     return false;
   }
-  if (deps.platform() === 'darwin' && args.appArgs.length === 0) {
+  if (args.appArgs.length === 0) {
     deps.launchAppBackgroundDetached(appPath, args.logLevel);
     return true;
   }
diff --git a/launcher/commands/command-modules.test.ts b/launcher/commands/command-modules.test.ts
index aaab9188..0d5ae93f 100644
--- a/launcher/commands/command-modules.test.ts
+++ b/launcher/commands/command-modules.test.ts
@@ -176,7 +176,25 @@ test('app command starts default macOS background app detached from launcher', (
   const calls: string[] = [];
 
   const handled = runAppPassthroughCommand(context, {
-    platform: () => 'darwin',
+    runAppCommandWithInherit: () => {
+      calls.push('attached');
+    },
+    launchAppBackgroundDetached: (appPath, logLevel) => {
+      calls.push(`detached:${appPath}:${logLevel}`);
+    },
+  });
+
+  assert.equal(handled, true);
+  assert.deepEqual(calls, ['detached:/tmp/subminer.app:info']);
+});
+
+test('app command starts default Linux background app detached from launcher', () => {
+  const context = createContext();
+  context.args.appPassthrough = true;
+  context.args.appArgs = [];
+  const calls: string[] = [];
+
+  const handled = runAppPassthroughCommand(context, {
     runAppCommandWithInherit: () => {
       calls.push('attached');
     },
@@ -197,7 +215,6 @@ test('app command keeps explicit passthrough args attached', () => {
   const detached: string[] = [];
 
   const handled = runAppPassthroughCommand(context, {
-    platform: () => 'darwin',
     runAppCommandWithInherit: (_appPath, appArgs) => {
       forwarded.push(appArgs);
     },
diff --git a/package.json b/package.json
index 8b3c957c..d9c23b54 100644
--- a/package.json
+++ b/package.json
@@ -50,7 +50,7 @@
     "test:plugin:src": "lua scripts/test-plugin-lua-compat.lua && lua scripts/test-plugin-start-gate.lua && lua scripts/test-plugin-session-bindings.lua && lua scripts/test-plugin-binary-windows.lua",
     "test:launcher:smoke:src": "bun test launcher/smoke.e2e.test.ts",
     "test:launcher:src": "bun test launcher/config.test.ts launcher/config-domain-parsers.test.ts launcher/config/cli-parser-builder.test.ts launcher/config/args-normalizer.test.ts launcher/mpv.test.ts launcher/picker.test.ts launcher/parse-args.test.ts launcher/main.test.ts launcher/commands/command-modules.test.ts launcher/commands/update-command.test.ts launcher/smoke.e2e.test.ts && bun run test:plugin:src",
-    "test:core:src": "bun test src/preload-settings.test.ts src/settings/settings-anki-controls.test.ts src/settings/settings-model.test.ts src/settings/settings-field-layout.test.ts src/cli/args.test.ts src/cli/help.test.ts src/shared/setup-state.test.ts src/core/services/cli-command.test.ts src/core/services/ipc.test.ts src/core/services/anki-jimaku-ipc.test.ts src/core/services/field-grouping-overlay.test.ts src/core/services/numeric-shortcut-session.test.ts src/core/services/secondary-subtitle.test.ts src/core/services/mpv-render-metrics.test.ts src/core/services/overlay-content-measurement.test.ts src/core/services/mpv-control.test.ts src/core/services/mpv.test.ts src/core/services/runtime-options-ipc.test.ts src/core/services/runtime-config.test.ts src/core/services/yomitan-extension-paths.test.ts src/core/services/yomitan-extension-loader.test.ts src/core/services/yomitan-settings.test.ts src/core/services/config-hot-reload.test.ts src/core/services/discord-presence.test.ts src/core/services/tokenizer.test.ts src/core/services/tokenizer/annotation-stage.test.ts src/core/services/tokenizer/parser-selection-stage.test.ts src/core/services/tokenizer/parser-enrichment-stage.test.ts src/core/services/subsync.test.ts src/core/services/overlay-bridge.test.ts src/core/services/overlay-shortcut-handler.test.ts src/core/services/stats-window.test.ts src/core/services/stats-window-lifecycle.test.ts src/core/services/__tests__/stats-server.test.ts src/main/runtime/stats-server-routing.test.ts src/core/services/mining.test.ts src/core/services/anki-jimaku.test.ts src/core/services/jimaku-download-path.test.ts src/core/services/jellyfin.test.ts src/core/services/jellyfin-remote.test.ts src/core/services/immersion-tracker-service.test.ts src/core/services/overlay-runtime-init.test.ts src/core/services/app-ready.test.ts src/core/services/startup-bootstrap.test.ts src/core/services/subtitle-processing-controller.test.ts src/main/runtime/current-subtitle-snapshot.test.ts src/main/runtime/autoplay-tokenization-warm-release.test.ts src/main/runtime/autoplay-subtitle-primer.test.ts src/core/services/anilist/anilist-update-queue.test.ts src/core/services/anilist/rate-limiter.test.ts src/core/services/jlpt-token-filter.test.ts src/core/services/subtitle-position.test.ts src/core/utils/shortcut-config.test.ts src/main/runtime/startup-mode-flags.test.ts src/main/runtime/first-run-setup-plugin.test.ts src/main/runtime/first-run-setup-service.test.ts src/main/runtime/first-run-setup-window.test.ts src/main/runtime/command-line-launcher.test.ts src/main/runtime/tray-runtime.test.ts src/main/runtime/tray-main-actions.test.ts src/main/runtime/tray-main-deps.test.ts src/main/runtime/tray-runtime-handlers.test.ts src/main/runtime/cli-command-context-main-deps.test.ts src/main/runtime/app-ready-main-deps.test.ts src/main/runtime/update/appimage-updater.test.ts src/main/runtime/update/fetch-adapter.test.ts src/main/runtime/update/release-metadata-policy.test.ts src/main/runtime/update/update-dialogs.test.ts src/main/runtime/update/support-assets.test.ts src/renderer/error-recovery.test.ts src/renderer/subtitle-render.test.ts src/renderer/subtitle-render-word-class.test.ts src/renderer/handlers/mouse.test.ts src/renderer/handlers/keyboard.test.ts src/renderer/modals/jimaku.test.ts src/subsync/utils.test.ts src/main/anilist-url-guard.test.ts src/window-trackers/hyprland-tracker.test.ts src/window-trackers/x11-tracker.test.ts src/window-trackers/windows-helper.test.ts src/window-trackers/windows-tracker.test.ts launcher/config.test.ts launcher/config-domain-parsers.test.ts launcher/config/cli-parser-builder.test.ts launcher/config/args-normalizer.test.ts launcher/parse-args.test.ts launcher/main.test.ts launcher/commands/command-modules.test.ts launcher/commands/update-command.test.ts launcher/setup-gate.test.ts stats/src/lib/api-client.test.ts stats/src/hooks/useExcludedWords.test.ts",
+    "test:core:src": "bun test src/preload-settings.test.ts src/settings/settings-anki-controls.test.ts src/settings/settings-model.test.ts src/settings/settings-field-layout.test.ts src/cli/args.test.ts src/cli/help.test.ts src/shared/setup-state.test.ts src/core/services/cli-command.test.ts src/core/services/ipc.test.ts src/core/services/anki-jimaku-ipc.test.ts src/core/services/field-grouping-overlay.test.ts src/core/services/numeric-shortcut-session.test.ts src/core/services/secondary-subtitle.test.ts src/core/services/mpv-render-metrics.test.ts src/core/services/overlay-content-measurement.test.ts src/core/services/mpv-control.test.ts src/core/services/mpv.test.ts src/core/services/runtime-options-ipc.test.ts src/core/services/runtime-config.test.ts src/core/services/yomitan-extension-paths.test.ts src/core/services/yomitan-extension-loader.test.ts src/core/services/yomitan-settings.test.ts src/core/services/settings-window-z-order.test.ts src/core/services/config-hot-reload.test.ts src/core/services/discord-presence.test.ts src/core/services/tokenizer.test.ts src/core/services/tokenizer/annotation-stage.test.ts src/core/services/tokenizer/parser-selection-stage.test.ts src/core/services/tokenizer/parser-enrichment-stage.test.ts src/core/services/subsync.test.ts src/core/services/overlay-bridge.test.ts src/core/services/overlay-shortcut-handler.test.ts src/core/services/stats-window.test.ts src/core/services/stats-window-lifecycle.test.ts src/core/services/__tests__/stats-server.test.ts src/main/runtime/stats-server-routing.test.ts src/core/services/mining.test.ts src/core/services/anki-jimaku.test.ts src/core/services/jimaku-download-path.test.ts src/core/services/jellyfin.test.ts src/core/services/jellyfin-remote.test.ts src/core/services/immersion-tracker-service.test.ts src/core/services/overlay-runtime-init.test.ts src/core/services/app-ready.test.ts src/core/services/startup-bootstrap.test.ts src/core/services/subtitle-processing-controller.test.ts src/main/runtime/current-subtitle-snapshot.test.ts src/main/runtime/autoplay-tokenization-warm-release.test.ts src/main/runtime/autoplay-subtitle-primer.test.ts src/core/services/anilist/anilist-update-queue.test.ts src/core/services/anilist/rate-limiter.test.ts src/core/services/jlpt-token-filter.test.ts src/core/services/subtitle-position.test.ts src/core/utils/shortcut-config.test.ts src/main/runtime/startup-mode-flags.test.ts src/main/runtime/config-settings-window.test.ts src/main/runtime/settings-window-z-order.test.ts src/main/runtime/setup-window-factory.test.ts src/main/runtime/first-run-setup-plugin.test.ts src/main/runtime/first-run-setup-service.test.ts src/main/runtime/first-run-setup-window.test.ts src/main/runtime/command-line-launcher.test.ts src/main/runtime/tray-runtime.test.ts src/main/runtime/tray-main-actions.test.ts src/main/runtime/tray-main-deps.test.ts src/main/runtime/tray-runtime-handlers.test.ts src/main/runtime/cli-command-context-main-deps.test.ts src/main/runtime/app-ready-main-deps.test.ts src/main/runtime/update/appimage-updater.test.ts src/main/runtime/update/fetch-adapter.test.ts src/main/runtime/update/release-metadata-policy.test.ts src/main/runtime/update/update-dialogs.test.ts src/main/runtime/update/support-assets.test.ts src/renderer/error-recovery.test.ts src/renderer/subtitle-render.test.ts src/renderer/subtitle-render-word-class.test.ts src/renderer/handlers/mouse.test.ts src/renderer/handlers/keyboard.test.ts src/renderer/modals/jimaku.test.ts src/subsync/utils.test.ts src/main/anilist-url-guard.test.ts src/window-trackers/hyprland-tracker.test.ts src/window-trackers/x11-tracker.test.ts src/window-trackers/windows-helper.test.ts src/window-trackers/windows-tracker.test.ts launcher/config.test.ts launcher/config-domain-parsers.test.ts launcher/config/cli-parser-builder.test.ts launcher/config/args-normalizer.test.ts launcher/parse-args.test.ts launcher/main.test.ts launcher/commands/command-modules.test.ts launcher/commands/update-command.test.ts launcher/setup-gate.test.ts stats/src/lib/api-client.test.ts stats/src/hooks/useExcludedWords.test.ts",
     "test:core:dist": "bun test dist/preload-settings.test.js dist/settings/settings-anki-controls.test.js dist/settings/settings-model.test.js dist/settings/settings-field-layout.test.js dist/cli/args.test.js dist/cli/help.test.js dist/core/services/cli-command.test.js dist/core/services/ipc.test.js dist/core/services/anki-jimaku-ipc.test.js dist/core/services/field-grouping-overlay.test.js dist/core/services/numeric-shortcut-session.test.js dist/core/services/secondary-subtitle.test.js dist/core/services/mpv-render-metrics.test.js dist/core/services/overlay-content-measurement.test.js dist/core/services/mpv-control.test.js dist/core/services/mpv.test.js dist/core/services/runtime-options-ipc.test.js dist/core/services/runtime-config.test.js dist/core/services/yomitan-extension-paths.test.js dist/core/services/config-hot-reload.test.js dist/core/services/discord-presence.test.js dist/core/services/tokenizer.test.js dist/core/services/tokenizer/annotation-stage.test.js dist/core/services/tokenizer/parser-selection-stage.test.js dist/core/services/tokenizer/parser-enrichment-stage.test.js dist/core/services/subsync.test.js dist/core/services/overlay-bridge.test.js dist/core/services/overlay-manager.test.js dist/core/services/overlay-shortcut-handler.test.js dist/core/services/stats-window-lifecycle.test.js dist/core/services/mining.test.js dist/core/services/anki-jimaku.test.js dist/core/services/jimaku-download-path.test.js dist/core/services/jellyfin.test.js dist/core/services/jellyfin-remote.test.js dist/core/services/immersion-tracker-service.test.js dist/core/services/overlay-runtime-init.test.js dist/core/services/app-ready.test.js dist/core/services/startup-bootstrap.test.js dist/core/services/subtitle-processing-controller.test.js dist/main/runtime/current-subtitle-snapshot.test.js dist/main/runtime/autoplay-tokenization-warm-release.test.js dist/main/runtime/autoplay-subtitle-primer.test.js dist/core/services/anilist/anilist-token-store.test.js dist/core/services/anilist/anilist-update-queue.test.js dist/core/services/anilist/rate-limiter.test.js dist/core/services/jlpt-token-filter.test.js dist/core/services/subtitle-position.test.js dist/renderer/error-recovery.test.js dist/renderer/subtitle-render.test.js dist/renderer/subtitle-render-word-class.test.js dist/renderer/handlers/mouse.test.js dist/renderer/handlers/keyboard.test.js dist/renderer/modals/jimaku.test.js dist/subsync/utils.test.js dist/main/anilist-url-guard.test.js dist/window-trackers/hyprland-tracker.test.js dist/window-trackers/x11-tracker.test.js dist/window-trackers/windows-helper.test.js dist/window-trackers/windows-tracker.test.js",
     "test:core:smoke:dist": "bun test dist/cli/help.test.js dist/core/services/runtime-config.test.js dist/core/services/ipc.test.js dist/core/services/overlay-manager.test.js dist/core/services/anilist/anilist-token-store.test.js dist/core/services/startup-bootstrap.test.js dist/renderer/error-recovery.test.js dist/main/anilist-url-guard.test.js dist/window-trackers/x11-tracker.test.js",
     "test:smoke:dist": "bun run test:config:smoke:dist && bun run test:core:smoke:dist",
diff --git a/src/core/services/index.ts b/src/core/services/index.ts
index 3b485e12..9becd0f1 100644
--- a/src/core/services/index.ts
+++ b/src/core/services/index.ts
@@ -28,6 +28,7 @@ export {
   shouldAutoInitializeOverlayRuntimeFromConfig,
 } from './startup';
 export { destroyYomitanSettingsWindow, openYomitanSettingsWindow } from './yomitan-settings';
+export { promoteSettingsWindowAboveOverlay } from './settings-window-z-order';
 export { createTokenizerDepsRuntime, tokenizeSubtitle } from './tokenizer';
 export {
   addYomitanNoteViaSearch,
diff --git a/src/core/services/settings-window-z-order.test.ts b/src/core/services/settings-window-z-order.test.ts
new file mode 100644
index 00000000..1516edfd
--- /dev/null
+++ b/src/core/services/settings-window-z-order.test.ts
@@ -0,0 +1,65 @@
+import assert from 'node:assert/strict';
+import test from 'node:test';
+import {
+  promoteSettingsWindowAboveOverlay,
+  shouldPromoteSettingsWindowAboveOverlay,
+} from './settings-window-z-order';
+
+test('settings window promotion only applies to Hyprland sessions', () => {
+  assert.equal(
+    shouldPromoteSettingsWindowAboveOverlay('linux', { HYPRLAND_INSTANCE_SIGNATURE: 'hypr' }),
+    true,
+  );
+  assert.equal(
+    shouldPromoteSettingsWindowAboveOverlay('linux', { WAYLAND_DISPLAY: 'wayland-1' }),
+    false,
+  );
+  assert.equal(
+    shouldPromoteSettingsWindowAboveOverlay('darwin', { HYPRLAND_INSTANCE_SIGNATURE: 'hypr' }),
+    false,
+  );
+});
+
+test('promoteSettingsWindowAboveOverlay raises Hyprland settings windows above the overlay', () => {
+  const calls: string[] = [];
+
+  const promoted = promoteSettingsWindowAboveOverlay(
+    {
+      isDestroyed: () => false,
+      getTitle: () => 'SubMiner Settings',
+      setAlwaysOnTop: (flag: boolean) => calls.push(`always-on-top:${flag}`),
+      moveTop: () => calls.push('move-top'),
+    } as never,
+    {
+      platform: 'linux',
+      env: { HYPRLAND_INSTANCE_SIGNATURE: 'hypr' },
+      ensureHyprlandWindowFloatingByTitle: ({ title }) => {
+        calls.push(`hyprland-top:${title}`);
+        return true;
+      },
+    },
+  );
+
+  assert.equal(promoted, true);
+  assert.deepEqual(calls, ['always-on-top:true', 'move-top', 'hyprland-top:SubMiner Settings']);
+});
+
+test('promoteSettingsWindowAboveOverlay skips destroyed windows', () => {
+  const calls: string[] = [];
+
+  const promoted = promoteSettingsWindowAboveOverlay(
+    {
+      isDestroyed: () => true,
+      getTitle: () => 'SubMiner Settings',
+      setAlwaysOnTop: () => calls.push('always-on-top'),
+      moveTop: () => calls.push('move-top'),
+    } as never,
+    {
+      platform: 'linux',
+      env: { HYPRLAND_INSTANCE_SIGNATURE: 'hypr' },
+    },
+  );
+
+  assert.equal(promoted, false);
+  assert.deepEqual(calls, []);
+});
diff --git a/src/core/services/settings-window-z-order.ts b/src/core/services/settings-window-z-order.ts
new file mode 100644
index 00000000..7f116edb
--- /dev/null
+++ b/src/core/services/settings-window-z-order.ts
@@ -0,0 +1,48 @@
+import type { BrowserWindow } from 'electron';
+import {
+  ensureHyprlandWindowFloatingByTitle,
+  shouldAttemptHyprlandWindowPlacement,
+} from './hyprland-window-placement';
+
+type SettingsWindowLevelController = Pick<
+  BrowserWindow,
+  'getTitle' | 'isDestroyed' | 'moveTop' | 'setAlwaysOnTop'
+>;
+
+type PromoteSettingsWindowOptions = {
+  platform?: NodeJS.Platform;
+  env?: NodeJS.ProcessEnv;
+  ensureHyprlandWindowFloatingByTitle?: typeof ensureHyprlandWindowFloatingByTitle;
+};
+
+export function shouldPromoteSettingsWindowAboveOverlay(
+  platform: NodeJS.Platform = process.platform,
+  env: NodeJS.ProcessEnv = process.env,
+): boolean {
+  return shouldAttemptHyprlandWindowPlacement(platform, env);
+}
+
+export function promoteSettingsWindowAboveOverlay(
+  window: SettingsWindowLevelController,
+  options: PromoteSettingsWindowOptions = {},
+): boolean {
+  const platform = options.platform ?? process.platform;
+  const env = options.env ?? process.env;
+  if (window.isDestroyed() || !shouldPromoteSettingsWindowAboveOverlay(platform, env)) {
+    return false;
+  }
+
+  window.setAlwaysOnTop(true);
+  window.moveTop();
+
+  const title = window.getTitle().trim();
+  if (title) {
+    (options.ensureHyprlandWindowFloatingByTitle ?? ensureHyprlandWindowFloatingByTitle)({
+      title,
+      platform,
+      env,
+    });
+  }
+
+  return true;
+}
diff --git a/src/core/services/yomitan-settings.test.ts b/src/core/services/yomitan-settings.test.ts
index 495615d3..2f047ae5 100644
--- a/src/core/services/yomitan-settings.test.ts
+++ b/src/core/services/yomitan-settings.test.ts
@@ -106,20 +106,32 @@ test('yomitan settings URL disables the embedded popup preview', () => {
 test('showYomitanSettingsWindow restores, repaints, shows, and focuses an existing window', () => {
   const calls: string[] = [];
 
-  showYomitanSettingsWindow({
-    isDestroyed: () => false,
-    isMinimized: () => true,
-    restore: () => calls.push('restore'),
-    getSize: () => [1200, 800],
-    setSize: (width: number, height: number) => calls.push(`set-size:${width}x${height}`),
-    webContents: {
-      invalidate: () => calls.push('invalidate'),
+  showYomitanSettingsWindow(
+    {
+      isDestroyed: () => false,
+      isMinimized: () => true,
+      restore: () => calls.push('restore'),
+      getSize: () => [1200, 800],
+      setSize: (width: number, height: number) => calls.push(`set-size:${width}x${height}`),
+      webContents: {
+        invalidate: () => calls.push('invalidate'),
+      },
+      show: () => calls.push('show'),
+      focus: () => calls.push('focus'),
+    } as never,
+    {
+      promoteSettingsWindowAboveOverlay: () => calls.push('promote'),
     },
-    show: () => calls.push('show'),
-    focus: () => calls.push('focus'),
-  } as never);
+  );
 
-  assert.deepEqual(calls, ['restore', 'set-size:1200x800', 'invalidate', 'show', 'focus']);
+  assert.deepEqual(calls, [
+    'restore',
+    'set-size:1200x800',
+    'invalidate',
+    'show',
+    'focus',
+    'promote',
+  ]);
 });
 
 test('destroyYomitanSettingsWindow destroys a live settings window before app quit', () => {
diff --git a/src/core/services/yomitan-settings.ts b/src/core/services/yomitan-settings.ts
index c5552182..8153c7dc 100644
--- a/src/core/services/yomitan-settings.ts
+++ b/src/core/services/yomitan-settings.ts
@@ -1,6 +1,7 @@
 import electron from 'electron';
 import type { BrowserWindow, Extension, Menu, MenuItemConstructorOptions, Session } from 'electron';
 import { createLogger } from '../../logger';
+import { promoteSettingsWindowAboveOverlay } from './settings-window-z-order';
 
 const { BrowserWindow: ElectronBrowserWindow, Menu: ElectronMenu, session } = electron;
 const logger = createLogger('main:yomitan-settings');
@@ -136,7 +137,12 @@ export function buildYomitanSettingsUrl(extensionId: string): string {
   return `chrome-extension://${extensionId}/settings.html?popup-preview=false`;
 }
 
-export function showYomitanSettingsWindow(settingsWindow: BrowserWindow): void {
+export function showYomitanSettingsWindow(
+  settingsWindow: BrowserWindow,
+  options: {
+    promoteSettingsWindowAboveOverlay?: (settingsWindow: BrowserWindow) => void;
+  } = {},
+): void {
   if (settingsWindow.isDestroyed()) {
     return;
   }
@@ -148,6 +154,7 @@ export function showYomitanSettingsWindow(settingsWindow: BrowserWindow): void {
   settingsWindow.webContents.invalidate();
   settingsWindow.show();
   settingsWindow.focus();
+  (options.promoteSettingsWindowAboveOverlay ?? promoteSettingsWindowAboveOverlay)(settingsWindow);
 }
 
 export function destroyYomitanSettingsWindow(settingsWindow: BrowserWindow | null): boolean {
@@ -177,6 +184,7 @@ export function openYomitanSettingsWindow(options: OpenYomitanSettingsWindowOpti
   logger.info('Creating new settings window for extension:', options.yomitanExt.id);
 
   const settingsWindow = new ElectronBrowserWindow({
+    title: 'Yomitan Settings',
     width: 1200,
     height: 800,
     show: false,
diff --git a/src/main.ts b/src/main.ts
index 19920485..1a94b4a9 100644
--- a/src/main.ts
+++ b/src/main.ts
@@ -332,6 +332,7 @@ import {
   mineSentenceCard as mineSentenceCardCore,
   openYomitanSettingsWindow,
   playNextSubtitleRuntime,
+  promoteSettingsWindowAboveOverlay,
   registerGlobalShortcuts as registerGlobalShortcutsCore,
   replayCurrentSubtitleRuntime,
   resolveJellyfinPlaybackPlanRuntime,
@@ -565,6 +566,7 @@ import {
   createCreateJellyfinSetupWindowHandler,
 } from './main/runtime/setup-window-factory';
 import { createConfigSettingsRuntime } from './main/runtime/config-settings-runtime';
+import { shouldSuppressVisibleOverlayRaiseForSeparateWindow } from './main/runtime/settings-window-z-order';
 import {
   isSameYoutubeMediaPath,
   isYoutubeMediaPath,
@@ -2034,6 +2036,8 @@ const configSettingsRuntime = createConfigSettingsRuntime({
     preloadPath: path.join(__dirname, 'preload-settings.js'),
   }),
   settingsHtmlPath: path.join(__dirname, 'settings', 'index.html'),
+  promoteSettingsWindowAboveOverlay: (window) =>
+    promoteSettingsWindowAboveOverlay(window as BrowserWindow),
   openPath: (targetPath) => shell.openPath(targetPath),
   ipcMain,
   ipcChannels: IPC_CHANNELS.request,
@@ -4927,8 +4931,17 @@ const updateVisibleOverlayBounds = createUpdateVisibleOverlayBoundsHandler(
 
 const buildEnsureOverlayWindowLevelMainDepsHandler =
   createBuildEnsureOverlayWindowLevelMainDepsHandler({
-    shouldSuppressOverlayWindowLevel: (window) =>
-      appState.statsOverlayVisible && window === overlayManager.getMainWindow(),
+    shouldSuppressOverlayWindowLevel: (window) => {
+      const mainWindow = overlayManager.getMainWindow();
+      return (
+        (appState.statsOverlayVisible && window === mainWindow) ||
+        shouldSuppressVisibleOverlayRaiseForSeparateWindow({
+          window,
+          mainWindow,
+          separateWindows: [appState.configSettingsWindow, appState.yomitanSettingsWindow],
+        })
+      );
+    },
     ensureOverlayWindowLevelCore: (window) => ensureOverlayWindowLevelCore(window as BrowserWindow),
     afterEnsureOverlayWindowLevel: () => {
       promoteStatsOverlayAbovePlayback();
diff --git a/src/main/runtime/config-settings-runtime.ts b/src/main/runtime/config-settings-runtime.ts
index 2376ec1a..002b4265 100644
--- a/src/main/runtime/config-settings-runtime.ts
+++ b/src/main/runtime/config-settings-runtime.ts
@@ -56,6 +56,7 @@ export interface ConfigSettingsRuntimeDeps<TWindow extends ConfigSettingsWindowL
   setSettingsWindow(window: TWindow | null): void;
   createSettingsWindow(): TWindow;
   settingsHtmlPath: string;
+  promoteSettingsWindowAboveOverlay?: (window: TWindow) => void;
   openPath(path: string): Promise<string>;
   defaultAnkiConnectUrl: string;
   createAnkiClient(url: string): ConfigSettingsAnkiClient;
@@ -144,6 +145,7 @@ export function createConfigSettingsRuntime<TWindow extends ConfigSettingsWindow
     setSettingsWindow: deps.setSettingsWindow,
     createSettingsWindow: deps.createSettingsWindow,
     settingsHtmlPath: deps.settingsHtmlPath,
+    promoteSettingsWindowAboveOverlay: deps.promoteSettingsWindowAboveOverlay,
     log: deps.log,
   });
 
diff --git a/src/main/runtime/config-settings-window.test.ts b/src/main/runtime/config-settings-window.test.ts
index 519a0157..d160ddeb 100644
--- a/src/main/runtime/config-settings-window.test.ts
+++ b/src/main/runtime/config-settings-window.test.ts
@@ -6,6 +6,7 @@ test('createOpenConfigSettingsWindowHandler focuses existing settings window', (
   const calls: string[] = [];
   const existing = {
     isDestroyed: () => false,
+    show: () => calls.push('show'),
     focus: () => calls.push('focus'),
     loadFile: () => calls.push('load'),
     on: () => {},
@@ -18,10 +19,11 @@ test('createOpenConfigSettingsWindowHandler focuses existing settings window', (
       throw new Error('Should not create a second window.');
     },
     settingsHtmlPath: '/tmp/settings.html',
+    promoteSettingsWindowAboveOverlay: () => calls.push('promote'),
   });
 
   assert.equal(open(), true);
-  assert.deepEqual(calls, ['focus']);
+  assert.deepEqual(calls, ['show', 'focus', 'promote']);
 });
 
 test('createOpenConfigSettingsWindowHandler creates window and clears closed state', () => {
@@ -29,6 +31,7 @@ test('createOpenConfigSettingsWindowHandler creates window and clears closed sta
   const handlers: { closed?: () => void } = {};
   const created = {
     isDestroyed: () => false,
+    show: () => calls.push('show'),
     focus: () => calls.push('focus'),
     loadFile: (path: string) => calls.push(`load:${path}`),
     on: (event: string, handler: () => void) => {
@@ -41,10 +44,11 @@ test('createOpenConfigSettingsWindowHandler creates window and clears closed sta
     setSettingsWindow: (window) => calls.push(window ? 'set:window' : 'set:null'),
     createSettingsWindow: () => created,
     settingsHtmlPath: '/tmp/settings.html',
+    promoteSettingsWindowAboveOverlay: () => calls.push('promote'),
   });
 
   assert.equal(open(), true);
-  assert.deepEqual(calls, ['load:/tmp/settings.html', 'set:window', 'focus']);
+  assert.deepEqual(calls, ['load:/tmp/settings.html', 'set:window', 'show', 'focus', 'promote']);
   assert.ok(handlers.closed);
   handlers.closed();
   assert.equal(calls.at(-1), 'set:null');
@@ -54,6 +58,7 @@ test('createOpenConfigSettingsWindowHandler clears failed load window state', as
   const calls: string[] = [];
   const created = {
     isDestroyed: () => false,
+    show: () => calls.push('show'),
     focus: () => calls.push('focus'),
     loadFile: (path: string) => {
       calls.push(`load:${path}`);
@@ -76,6 +81,7 @@ test('createOpenConfigSettingsWindowHandler clears failed load window state', as
   assert.deepEqual(calls, [
     'load:/tmp/missing-settings.html',
     'set:window',
+    'show',
     'focus',
     'set:null',
     'destroy',
diff --git a/src/main/runtime/config-settings-window.ts b/src/main/runtime/config-settings-window.ts
index a3167291..7ac20a13 100644
--- a/src/main/runtime/config-settings-window.ts
+++ b/src/main/runtime/config-settings-window.ts
@@ -1,5 +1,6 @@
 export interface ConfigSettingsWindowLike {
   isDestroyed(): boolean;
+  show(): void;
   focus(): void;
   loadFile(path: string): unknown;
   on(event: 'closed', handler: () => void): unknown;
@@ -11,6 +12,7 @@ export interface OpenConfigSettingsWindowDeps<TWindow extends ConfigSettingsWind
   setSettingsWindow(window: TWindow | null): void;
   createSettingsWindow(): TWindow;
   settingsHtmlPath: string;
+  promoteSettingsWindowAboveOverlay?: (window: TWindow) => void;
   log?: (message: string) => void;
 }
 
@@ -18,9 +20,15 @@ export function createOpenConfigSettingsWindowHandler<TWindow extends ConfigSett
   deps: OpenConfigSettingsWindowDeps<TWindow>,
 ): () => boolean {
   return () => {
+    const showAndFocus = (window: TWindow): void => {
+      window.show();
+      window.focus();
+      deps.promoteSettingsWindowAboveOverlay?.(window);
+    };
+
     const existing = deps.getSettingsWindow();
     if (existing && !existing.isDestroyed()) {
-      existing.focus();
+      showAndFocus(existing);
       return true;
     }
 
@@ -35,7 +43,7 @@ export function createOpenConfigSettingsWindowHandler<TWindow extends ConfigSett
     window.on('closed', () => {
       deps.setSettingsWindow(null);
     });
-    window.focus();
+    showAndFocus(window);
     return true;
   };
 }
diff --git a/src/main/runtime/settings-window-z-order.test.ts b/src/main/runtime/settings-window-z-order.test.ts
new file mode 100644
index 00000000..990eafd5
--- /dev/null
+++ b/src/main/runtime/settings-window-z-order.test.ts
@@ -0,0 +1,40 @@
+import assert from 'node:assert/strict';
+import test from 'node:test';
+import { shouldSuppressVisibleOverlayRaiseForSeparateWindow } from './settings-window-z-order';
+
+test('separate settings windows suppress visible overlay restacking', () => {
+  const mainWindow = { id: 'overlay', isDestroyed: () => false };
+  const settingsWindow = { id: 'settings', isDestroyed: () => false };
+
+  assert.equal(
+    shouldSuppressVisibleOverlayRaiseForSeparateWindow({
+      window: mainWindow,
+      mainWindow,
+      separateWindows: [settingsWindow],
+    }),
+    true,
+  );
+});
+
+test('separate settings windows do not suppress unrelated or closed overlay work', () => {
+  const mainWindow = { id: 'overlay', isDestroyed: () => false };
+  const modalWindow = { id: 'modal', isDestroyed: () => false };
+  const closedSettingsWindow = { id: 'settings', isDestroyed: () => true };
+
+  assert.equal(
+    shouldSuppressVisibleOverlayRaiseForSeparateWindow({
+      window: modalWindow,
+      mainWindow,
+      separateWindows: [{ isDestroyed: () => false }],
+    }),
+    false,
+  );
+  assert.equal(
+    shouldSuppressVisibleOverlayRaiseForSeparateWindow({
+      window: mainWindow,
+      mainWindow,
+      separateWindows: [closedSettingsWindow, null],
+    }),
+    false,
+  );
+});
diff --git a/src/main/runtime/settings-window-z-order.ts b/src/main/runtime/settings-window-z-order.ts
new file mode 100644
index 00000000..d6cbc311
--- /dev/null
+++ b/src/main/runtime/settings-window-z-order.ts
@@ -0,0 +1,19 @@
+type SeparateWindowLike = {
+  isDestroyed(): boolean;
+};
+
+function hasLiveSeparateWindow(windows: Array<SeparateWindowLike | null | undefined>): boolean {
+  return windows.some((window) => Boolean(window && !window.isDestroyed()));
+}
+
+export function shouldSuppressVisibleOverlayRaiseForSeparateWindow(options: {
+  window: unknown;
+  mainWindow: unknown;
+  separateWindows: Array<SeparateWindowLike | null | undefined>;
+}): boolean {
+  if (!options.mainWindow || options.window !== options.mainWindow) {
+    return false;
+  }
+
+  return hasLiveSeparateWindow(options.separateWindows);
+}
diff --git a/src/main/runtime/setup-window-factory.test.ts b/src/main/runtime/setup-window-factory.test.ts
index e323c3de..059b1d0c 100644
--- a/src/main/runtime/setup-window-factory.test.ts
+++ b/src/main/runtime/setup-window-factory.test.ts
@@ -111,7 +111,7 @@ test('createCreateConfigSettingsWindowHandler builds configuration settings wind
     width: 1040,
     height: 760,
     title: 'SubMiner Settings',
-    show: true,
+    show: false,
     autoHideMenuBar: true,
     resizable: true,
     backgroundColor: '#24273a',
diff --git a/src/main/runtime/setup-window-factory.ts b/src/main/runtime/setup-window-factory.ts
index 02ac42a7..08e5227a 100644
--- a/src/main/runtime/setup-window-factory.ts
+++ b/src/main/runtime/setup-window-factory.ts
@@ -2,6 +2,7 @@ interface SetupWindowConfig {
   width: number;
   height: number;
   title: string;
+  show?: boolean;
   resizable?: boolean;
   minimizable?: boolean;
   maximizable?: boolean;
@@ -19,7 +20,7 @@ function createSetupWindowHandler<TWindow>(
       width: config.width,
       height: config.height,
       title: config.title,
-      show: true,
+      show: config.show ?? true,
       autoHideMenuBar: true,
       ...(config.resizable === undefined ? {} : { resizable: config.resizable }),
       ...(config.minimizable === undefined ? {} : { minimizable: config.minimizable }),
@@ -77,6 +78,7 @@ export function createCreateConfigSettingsWindowHandler<TWindow>(deps: {
     width: 1040,
     height: 760,
     title: 'SubMiner Settings',
+    show: false,
     resizable: true,
     preloadPath: deps.preloadPath,
     backgroundColor: '#24273a',