diff --git a/package-lock.json b/package-lock.json
index 761f5ac..2c0c465 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -23,6 +23,7 @@
       "devDependencies": {
         "@tailwindcss/postcss": "^4.1.18",
         "@tauri-apps/cli": "^2.10.0",
+        "@types/node": "^25.2.3",
         "@types/react": "^19.2.13",
         "@types/react-dom": "^19.2.3",
         "@types/react-window": "^2.0.0",
@@ -2039,6 +2040,16 @@
       "dev": true,
       "license": "MIT"
     },
+    "node_modules/@types/node": {
+      "version": "25.2.3",
+      "resolved": "https://registry.npmjs.org/@types/node/-/node-25.2.3.tgz",
+      "integrity": "sha512-m0jEgYlYz+mDJZ2+F4v8D1AyQb+QzsNqRuI7xg1VQX/KlKS0qT9r1Mo16yo5F/MtifXFgaofIFsdFMox2SxIbQ==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "undici-types": "~7.16.0"
+      }
+    },
     "node_modules/@types/react": {
       "version": "19.2.13",
       "resolved": "https://registry.npmjs.org/@types/react/-/react-19.2.13.tgz",
@@ -4152,6 +4163,13 @@
         "typescript": ">=4.8.4 <6.0.0"
       }
     },
+    "node_modules/undici-types": {
+      "version": "7.16.0",
+      "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-7.16.0.tgz",
+      "integrity": "sha512-Zz+aZWSj8LE6zoxD+xrjh4VfkIG8Ya6LvYkZqtUQGJPZjYl53ypCaUwWqo7eI0x66KBGeRo+mlBEkMSeSZ38Nw==",
+      "dev": true,
+      "license": "MIT"
+    },
     "node_modules/update-browserslist-db": {
       "version": "1.2.2",
       "resolved": "https://registry.npmjs.org/update-browserslist-db/-/update-browserslist-db-1.2.2.tgz",
diff --git a/package.json b/package.json
index ab864ec..4036df6 100644
--- a/package.json
+++ b/package.json
@@ -43,6 +43,7 @@
   "devDependencies": {
     "@tailwindcss/postcss": "^4.1.18",
     "@tauri-apps/cli": "^2.10.0",
+    "@types/node": "^25.2.3",
     "@types/react": "^19.2.13",
     "@types/react-dom": "^19.2.3",
     "@types/react-window": "^2.0.0",
diff --git a/scripts/install.sh b/scripts/install.sh
index 3cd0346..c0d759a 100755
--- a/scripts/install.sh
+++ b/scripts/install.sh
@@ -439,8 +439,6 @@ sanitize_xdg_data_dirs() {
 }
 sanitize_xdg_data_dirs
 
-export GDK_SCALE="${GDK_SCALE:-1}"
-export GDK_DPI_SCALE="${GDK_DPI_SCALE:-1}"
 export NO_AT_BRIDGE=1
 
 exec "$HOME/.local/bin/win11-clipboard-history.AppImage" "$@"
diff --git a/src-tauri/bundle/linux/wrapper.sh b/src-tauri/bundle/linux/wrapper.sh
index f8ec246..48d6f18 100755
--- a/src-tauri/bundle/linux/wrapper.sh
+++ b/src-tauri/bundle/linux/wrapper.sh
@@ -139,8 +139,6 @@ fi
 # ---------------------------------------------------------------------------
 # Display & rendering defaults
 # ---------------------------------------------------------------------------
-export GDK_SCALE="${GDK_SCALE:-1}"
-export GDK_DPI_SCALE="${GDK_DPI_SCALE:-1}"
 
 export TAURI_TRAY="${TAURI_TRAY:-libayatana-appindicator3}"
 
diff --git a/src-tauri/src/main.rs b/src-tauri/src/main.rs
index f4a43d1..20c2bf1 100644
--- a/src-tauri/src/main.rs
+++ b/src-tauri/src/main.rs
@@ -274,6 +274,30 @@ async fn copy_text_to_clipboard(_state: State<'_, AppState>, text: String) -> Re
     Ok(())
 }
 
+#[tauri::command]
+async fn finish_setup(app: AppHandle) -> Result<(), String> {
+    // 1. Mark first run as complete (redundant but safe)
+    win11_clipboard_history_lib::permission_checker::mark_first_run_complete()
+        .map_err(|e| e.to_string())?;
+
+    // 2. Close setup window
+    if let Some(setup_window) = app.get_webview_window("setup") {
+        let _ = setup_window.close();
+    }
+
+    // 3. Show main window
+    if let Some(main_window) = app.get_webview_window("main") {
+        // Ensure it's ready to be shown
+        WindowController::position_and_show(&main_window, &app);
+    }
+
+    // 4. Emit event to main window to update its state (stop waiting)
+    // We emit to all just in case, or specifically to main
+    let _ = app.emit("setup_complete", ());
+
+    Ok(())
+}
+
 // --- Helper for Paste Logic ---
 
 struct PasteHelper;
@@ -773,6 +797,19 @@ fn main() {
             config_manager: config_manager.clone(),
             is_mouse_inside: is_mouse_inside.clone(),
         })
+        .on_window_event(|window, event| {
+            if let tauri::WindowEvent::Destroyed = event {
+                if window.label() == "setup" {
+                    // Check if setup was effectively finished.
+                    // If the user clicked "Start Using", `finish_setup` would have been called.
+                    // `finish_setup` calls `mark_first_run_complete`.
+                    if win11_clipboard_history_lib::permission_checker::is_first_run() {
+                         println!("[Setup] Setup window closed without completion. Exiting app.");
+                         window.app_handle().exit(0);
+                    }
+                }
+            }
+        })
         .setup(move |app| {
             let app_handle = app.handle().clone();
 
@@ -985,6 +1022,7 @@ fn main() {
             get_recent_emojis,
             paste_gif_from_url,
             finish_paste,
+            finish_setup, // Register the new command
             set_mouse_state,
             get_user_settings,
             set_user_settings,
diff --git a/src-tauri/tauri.conf.json b/src-tauri/tauri.conf.json
index c60715d..e0addc1 100644
--- a/src-tauri/tauri.conf.json
+++ b/src-tauri/tauri.conf.json
@@ -31,6 +31,22 @@
         "alwaysOnTop": true,
         "focus": true
       },
+      {
+        "title": "Setup - Clipboard History",
+        "label": "setup",
+        "width": 550,
+        "height": 650,
+        "resizable": true,
+        "minWidth": 400,
+        "minHeight": 500,
+        "decorations": true,
+        "transparent": false,
+        "visible": false,
+        "skipTaskbar": false,
+        "alwaysOnTop": false,
+        "center": true,
+        "focus": true
+      },
       {
         "title": "Settings - Clipboard History",
         "label": "settings",
@@ -52,7 +68,11 @@
   },
   "bundle": {
     "active": true,
-    "targets": ["deb", "rpm", "appimage"],
+    "targets": [
+      "deb",
+      "rpm",
+      "appimage"
+    ],
     "icon": [
       "icons/32x32.png",
       "icons/64x64.png",
@@ -104,6 +124,8 @@
         "preRemoveScript": "bundle/linux/postrm.sh"
       }
     },
-    "resources": ["bundle/linux/99-win11-clipboard-input.rules"]
+    "resources": [
+      "bundle/linux/99-win11-clipboard-input.rules"
+    ]
   }
-}
+}
\ No newline at end of file
diff --git a/src/components/SetupWizard.tsx b/src/components/SetupWizard.tsx
index 58a7d22..b90859f 100644
--- a/src/components/SetupWizard.tsx
+++ b/src/components/SetupWizard.tsx
@@ -666,22 +666,19 @@ export function SetupWizard({ onComplete }: SetupWizardProps) {
   }
 
   return (
-    <div className="fixed inset-0 flex items-center justify-center z-50 p-4">
-      {/* Backdrop */}
-      <div className="absolute inset-0 bg-black/50 backdrop-blur-sm" />
-
-      {/* Modal */}
-      <div
-        className={clsx(
-          'relative w-full max-w-sm rounded-win11-lg p-6 shadow-win11-elevated animate-scale-in',
-          isDark ? 'glass-effect' : 'glass-effect-light',
-          isDark ? 'text-win11-text-primary' : 'text-win11Light-text-primary'
-        )}
-      >
+    <div
+      className={clsx(
+        'h-full w-full flex flex-col items-center justify-center p-6',
+        isDark
+          ? 'bg-win11-bg-primary text-win11-text-primary'
+          : 'bg-win11Light-bg-primary text-win11Light-text-primary'
+      )}
+    >
+      <div className={clsx('w-full max-w-sm', 'animate-scale-in')}>
         {steps[step]}
 
         {/* Progress dots */}
-        <div className="flex justify-center gap-2 mt-6">
+        <div className="flex justify-center gap-2 mt-8">
           {steps.map((_, i) => (
             <button
               key={`dot-${i}`}
diff --git a/src/main.tsx b/src/main.tsx
index 8677ac4..d7b036d 100644
--- a/src/main.tsx
+++ b/src/main.tsx
@@ -1,75 +1,81 @@
 import React, { useState, useEffect } from 'react'
 import ReactDOM from 'react-dom/client'
-import { getCurrentWindow } from '@tauri-apps/api/window'
+import { getCurrentWindow, getAllWindows } from '@tauri-apps/api/window'
+import { WebviewWindow } from '@tauri-apps/api/webviewWindow'
 import { invoke } from '@tauri-apps/api/core'
 import { listen } from '@tauri-apps/api/event'
 import ClipboardApp from './ClipboardApp'
 import SettingsApp from './SettingsApp'
-import { SetupWizard } from './components/SetupWizard'
+import { SetupApp } from './setup'
 import './index.css'
 
 /**
- * Main app wrapper that handles first-run setup wizard
+ * Main app wrapper that handles first-run check and launches setup window if needed
  */
 function ClipboardAppWithSetup() {
-  const [showWizard, setShowWizard] = useState(false)
   const [loading, setLoading] = useState(true)
+  const [waitingForSetup, setWaitingForSetup] = useState(false)
 
   useEffect(() => {
-    // Check if this is first run
-    invoke<boolean>('is_first_run')
-      .then((isFirst) => {
-        setShowWizard(isFirst)
-        setLoading(false)
+    let unlistenSetup: (() => void) | undefined
+
+    const init = async () => {
+      // Listen for setup completion event from the setup window
+      // We set this up early to ensure we don't miss it
+      unlistenSetup = await listen('setup_complete', async () => {
+        console.log('Setup complete event received')
+        setWaitingForSetup(false)
       })
-      .catch((err) => {
+
+      // Check if this is first run
+      try {
+        const isFirst = await invoke<boolean>('is_first_run')
+        if (isFirst) {
+          setWaitingForSetup(true)
+
+          // In Tauri v2, if the window is in tauri.conf.json, it's already created.
+          // We just need to find it and show it.
+          const windows = await getAllWindows()
+          const setupWin = windows.find((w) => w.label === 'setup')
+
+          if (setupWin) {
+            await setupWin.show()
+            await setupWin.setFocus()
+          } else {
+            console.error('Setup window not found in config')
+            // Attempt to create it if it somehow doesn't exist (fallback)
+            const newSetupWin = new WebviewWindow('setup')
+            newSetupWin.once('tauri://created', () => {
+              newSetupWin.show()
+              newSetupWin.setFocus()
+            })
+          }
+        }
+        setLoading(false)
+      } catch (err: unknown) {
         console.error('Failed to check first run:', err)
         setLoading(false)
-      })
-
-    // Listen for reset-to-defaults event from settings
-    let isMounted = true
-    let unlistenFn: (() => void) | null = null
-
-    listen('show-setup-wizard', () => {
-      if (isMounted) {
-        setShowWizard(true)
       }
-    }).then((fn) => {
-      if (isMounted) {
-        unlistenFn = fn
-      } else {
-        // Component already unmounted, clean up immediately
-        fn()
-      }
-    })
+    }
+
+    init()
 
     return () => {
-      isMounted = false
-      unlistenFn?.()
+      if (unlistenSetup) unlistenSetup()
     }
   }, [])
 
-  const handleWizardComplete = () => {
-    setShowWizard(false)
-  }
-
-  if (loading) {
-    // Show nothing while checking first run status
+  if (loading || waitingForSetup) {
+    // Show nothing while checking status or waiting for setup to complete
+    // This prevents the clipboard app from trying to initialize before permissions are granted
     return null
   }
 
-  return (
-    <>
-      {showWizard && <SetupWizard onComplete={handleWizardComplete} />}
-      <ClipboardApp />
-    </>
-  )
+  return <ClipboardApp />
 }
 
 /**
- * Root component that routes to either ClipboardApp or SettingsApp
- * based on the current window's label
+ * Root component that routes based on the current window's label
  */
 export default function Root() {
   const [windowLabel] = useState<string>(() => getCurrentWindow().label)
@@ -79,7 +85,11 @@ export default function Root() {
     return <SettingsApp />
   }
 
-  // Default to ClipboardApp with setup wizard for 'main' and any other window
+  if (windowLabel === 'setup') {
+    return <SetupApp />
+  }
+
+  // Default to ClipboardAppWithSetup for 'main'
   return <ClipboardAppWithSetup />
 }
 
diff --git a/src/setup.tsx b/src/setup.tsx
new file mode 100644
index 0000000..95ff167
--- /dev/null
+++ b/src/setup.tsx
@@ -0,0 +1,27 @@
+import { SetupWizard } from './components/SetupWizard'
+import './index.css'
+import { invoke } from '@tauri-apps/api/core'
+
+export function SetupApp() {
+  const handleComplete = async () => {
+    try {
+      console.log('SetupApp: invoking finish_setup command')
+      await invoke('finish_setup')
+    } catch (err) {
+      console.error('Failed to finish setup:', err)
+      // Do not close the window on failure; keep it open so the user can retry.
+      // If we close it while first_run is still true, the backend will exit the app.
+      if (typeof window !== 'undefined') {
+        alert('Failed to finish setup. Please try again or check the logs for details.')
+      }
+    }
+  }
+
+  return (
+    <div className="h-screen w-screen overflow-hidden bg-transparent">
+      {/* Pass handleComplete which invokes the backend finish_setup command 
+            to mark setup as done, close this window, and show the main app. */}
+      <SetupWizard onComplete={handleComplete} />
+    </div>
+  )
+}
diff --git a/src/utils/systemTheme.ts b/src/utils/systemTheme.ts
index c8021e1..cd0c15e 100644
--- a/src/utils/systemTheme.ts
+++ b/src/utils/systemTheme.ts
@@ -78,7 +78,7 @@ export function useSystemThemePreference(): boolean {
 
       if (!hasEventListener) {
         // Event listener not available, use polling fallback
-        checkInterval = setInterval(async () => {
+        checkInterval = window.setInterval(async () => {
           const portalPrefersDark = await getSystemThemeFromPortal()
           if (portalPrefersDark !== null) {
             setSystemPrefersDark(portalPrefersDark)
diff --git a/vite.config.ts b/vite.config.ts
index 0fcc522..f3c868f 100644
--- a/vite.config.ts
+++ b/vite.config.ts
@@ -4,7 +4,7 @@ import react from '@vitejs/plugin-react'
 // https://vitejs.dev/config/
 export default defineConfig({
   plugins: [react()],
-  
+
   // Tauri expects a fixed port for development
   server: {
     port: 1420,
@@ -28,5 +28,10 @@ export default defineConfig({
     minify: !process.env.TAURI_DEBUG ? 'esbuild' : false,
     // Produce sourcemaps for debug builds
     sourcemap: !!process.env.TAURI_DEBUG,
+    rollupOptions: {
+      input: {
+        main: 'index.html',
+      },
+    },
   },
 })