diff --git a/application/src/electron/main.ts b/application/src/electron/main.ts
index 307cda5c..4be685e2 100644
--- a/application/src/electron/main.ts
+++ b/application/src/electron/main.ts
@@ -197,7 +197,10 @@ async function handleLaunchHooks(
   if (mainWindow) {
     registerMainHandlers(mainWindow);
     await startAddonRuntime();
-    await runStartupTasks(mainWindow);
+    const startupResult = await runStartupTasks(mainWindow);
+    if (startupResult.shutdownPending) {
+      return;
+    }
 
     // Load the main app with game ID and hook flags
     const baseUrl = isDev()
@@ -232,7 +235,10 @@ async function launchGameById(gameId: number, wrapperCommand?: string | null) {
     registerMainHandlers(mainWindow);
     await startAddonRuntime();
     // Run startup tasks first
-    await runStartupTasks(mainWindow);
+    const startupResult = await runStartupTasks(mainWindow);
+    if (startupResult.shutdownPending) {
+      return;
+    }
 
     // Load the main app with the game ID in the query params
     // The Svelte frontend will detect this and show the GameLaunchOverlay
@@ -592,8 +598,14 @@ function createWindow(options: { gameLaunchMode?: boolean } = {}) {
 
 async function startAppFlow(win: BrowserWindow) {
   // Run startup tasks; splash updates go to the main window
+  let shutdownPending = false;
   if (win && !win.isDestroyed()) {
-    await runStartupTasks(win);
+    const startupResult = await runStartupTasks(win);
+    shutdownPending = startupResult.shutdownPending;
+  }
+
+  if (shutdownPending) {
+    return;
   }
 
   // Load the main app into the same window (replaces splash)
diff --git a/application/src/electron/startup-runner.ts b/application/src/electron/startup-runner.ts
index dfb31c32..c5645b54 100644
--- a/application/src/electron/startup-runner.ts
+++ b/application/src/electron/startup-runner.ts
@@ -1,7 +1,10 @@
 import { app, BrowserWindow } from 'electron';
 import { join } from 'path';
 import type { UpdaterCallbacks } from '@/electron/updater.js';
-import { createDefaultSystemUpdateManager } from '@/electron/system-updater.js';
+import {
+  createDefaultSystemUpdateManager,
+  type SystemUpdateResult,
+} from '@/electron/system-updater.js';
 import {
   restoreBackup,
   removeCachedAppUpdates,
@@ -91,6 +94,15 @@ export function closeSplashWindow() {
   }
 }
 
+export type StartupTasksResult = {
+  /** When true, an installer update is shutting the app down; do not load the main UI. */
+  shutdownPending: boolean;
+};
+
+function isShutdownPendingFromUpdates(results: SystemUpdateResult[]): boolean {
+  return results.some((result) => result.updated === true);
+}
+
 /**
  * Runs all pre-launch startup tasks with splash screen feedback.
  * This includes restoring backups, running migrations, checking for updates, etc.
@@ -103,7 +115,8 @@ export function closeSplashWindow() {
  */
 export async function runStartupTasks(
   mainWindow?: BrowserWindow | null
-): Promise<void> {
+): Promise<StartupTasksResult> {
+  let shutdownPending = false;
   try {
     if (mainWindow && !mainWindow.isDestroyed()) {
       splashTargetWindow = mainWindow;
@@ -165,15 +178,24 @@ export async function runStartupTasks(
         updateSplashProgress(current, total, speed);
       },
     };
-    await createDefaultSystemUpdateManager().updateOnlineSystem(
-      updaterCallbacks
-    );
+    const updateResults =
+      await createDefaultSystemUpdateManager().updateOnlineSystem(
+        updaterCallbacks
+      );
 
-    // Final status before main window loads
-    updateSplashStatus('Starting application...');
+    shutdownPending = isShutdownPendingFromUpdates(updateResults);
+
+    // Final status before main window loads (skip when installer update will exit)
+    if (!shutdownPending) {
+      updateSplashStatus('Starting application...');
+    }
   } finally {
-    splashTargetWindow = null;
-    // Ensure splash window is closed if it was created
-    closeSplashWindow();
+    if (!shutdownPending) {
+      splashTargetWindow = null;
+      // Ensure splash window is closed if it was created
+      closeSplashWindow();
+    }
   }
+
+  return { shutdownPending };
 }
diff --git a/application/src/electron/startup.ts b/application/src/electron/startup.ts
index d53f444b..826bdb09 100644
--- a/application/src/electron/startup.ts
+++ b/application/src/electron/startup.ts
@@ -446,6 +446,20 @@ export async function restoreBackup(
     return { needsAddonReinstall: false };
   }
 
+  if (process.platform === 'linux') {
+    console.log('[backup] Skipping setup backup restore on Linux.');
+    try {
+      rmSync(backupDir, { recursive: true, force: true });
+      console.log('[backup] Removed stale Linux update backup.');
+    } catch (deleteError: any) {
+      console.warn(
+        '[backup] Could not delete stale Linux update backup:',
+        deleteError.message
+      );
+    }
+    return { needsAddonReinstall: false };
+  }
+
   const flagPath = join(backupDir, 'needs-addon-reinstall.flag');
   needsAddonReinstall = existsSync(flagPath);
 
@@ -469,7 +483,7 @@ export async function restoreBackup(
     return { needsAddonReinstall };
   }
 
-  // Check for addon reinstall flag (works for both Windows and Linux)
+  // Check for addon reinstall flag.
   if (needsAddonReinstall) {
     needsAddonReinstall = true;
     console.log('[backup] Addon reinstall flag found');
diff --git a/application/src/electron/updater.ts b/application/src/electron/updater.ts
index fc093d42..d6a53e6e 100644
--- a/application/src/electron/updater.ts
+++ b/application/src/electron/updater.ts
@@ -23,8 +23,8 @@ import { spawn, exec } from 'child_process';
 import { createHash } from 'crypto';
 import * as zlib from 'zlib';
 import * as path from 'path';
-import { __dirname as persistentDataDir } from '@/electron/manager/manager.paths.js';
 import { getEffectiveOnlineState } from '@/electron/lib/online.js';
+import { __dirname } from '@/electron/manager/manager.paths.js';
 
 function isDev() {
   return !app.isPackaged;
@@ -52,10 +52,6 @@ if (process.platform === 'linux') {
   __dirname = './';
 }
 
-function getBackupSourceRoot() {
-  return process.platform === 'linux' ? persistentDataDir : __dirname;
-}
-
 /**
  * Counts the total number of files to backup, excluding specified directories.
  */
@@ -151,7 +147,7 @@ async function backupFilesAsync(
   updateStatus: (text: string, subtext?: string) => void,
   updateProgress: (current: number, total: number, speed: string) => void
 ): Promise<{ success: boolean; needsAddonReinstall: boolean }> {
-  const sourceRoot = getBackupSourceRoot();
+  const sourceRoot = __dirname;
 
   // First, count total files to backup
   let totalFiles = 0;
@@ -591,6 +587,20 @@ async function backupStateForSetupReplacement(
   updateProgress: (current: number, total: number, speed: string) => void
 ) {
   const tempFolder = join(app.getPath('temp'), 'ogi-update-backup');
+
+  if (process.platform === 'linux') {
+    console.log('[updater] Skipping setup backup on Linux.');
+    try {
+      rmSync(tempFolder, { recursive: true, force: true });
+    } catch (cleanupError: any) {
+      console.warn(
+        '[updater] Failed to clean stale Linux update backup:',
+        cleanupError.message
+      );
+    }
+    return;
+  }
+
   updateStatus('Backing up Files', 'Calculating...');
 
   try {
@@ -868,8 +878,6 @@ export function checkIfInstallerUpdateAvailable(
             updateProgress,
           });
           console.log(`[updater] Setup downloaded successfully.`);
-          console.log(`[updater] Backing up files in update.`);
-          await backupStateForSetupReplacement(updateStatus, updateProgress);
 
           updateStatus('Starting Setup');