diff --git a/apps/desktop/.gitignore b/apps/desktop/.gitignore
index 43ffb2d1436..4e5d8ab2674 100644
--- a/apps/desktop/.gitignore
+++ b/apps/desktop/.gitignore
@@ -9,6 +9,7 @@
 # production
 /build
 /dist
+/.native-modules
 
 # misc
 .DS_Store
diff --git a/apps/desktop/electron-builder.ts b/apps/desktop/electron-builder.ts
index 033ccef42c4..d37e722218b 100644
--- a/apps/desktop/electron-builder.ts
+++ b/apps/desktop/electron-builder.ts
@@ -38,8 +38,14 @@ const config: Configuration = {
 			to: "resources",
 			filter: ["**/*"],
 		},
-		// Only include node-pty (native module that can't be bundled)
-		"node_modules/node-pty/**/*",
+		// Native module that can't be bundled by Vite.
+		// The copy:native-modules script replaces symlinks with real files
+		// before building (required for Bun 1.3+ isolated installs).
+		{
+			from: "node_modules/node-pty",
+			to: "node_modules/node-pty",
+			filter: ["**/*"],
+		},
 		"!**/.DS_Store",
 	],
 
diff --git a/apps/desktop/package.json b/apps/desktop/package.json
index 356161d0812..b9924261735 100644
--- a/apps/desktop/package.json
+++ b/apps/desktop/package.json
@@ -18,8 +18,10 @@
 		"predev": "bun run clean:dev",
 		"dev": "cross-env NODE_ENV=development electron-vite dev --watch",
 		"compile:app": "electron-vite build",
-		"prebuild": "bun run clean:dev && bun run compile:app",
+		"copy:native-modules": "bun run scripts/copy-native-modules.ts",
+		"prebuild": "bun run clean:dev && bun run compile:app && bun run copy:native-modules",
 		"build": "electron-builder",
+		"prepackage": "bun run copy:native-modules",
 		"package": "electron-builder --config electron-builder.ts",
 		"install:deps": "electron-builder install-app-deps",
 		"make:release": "tsx ./src/lib/electron-app/release/modules/release.ts",
diff --git a/apps/desktop/scripts/copy-native-modules.ts b/apps/desktop/scripts/copy-native-modules.ts
new file mode 100644
index 00000000000..531e6fc3d7b
--- /dev/null
+++ b/apps/desktop/scripts/copy-native-modules.ts
@@ -0,0 +1,57 @@
+/**
+ * Prepare native modules for electron-builder.
+ *
+ * With Bun 1.3+ isolated installs, node_modules contains symlinks to packages
+ * stored in node_modules/.bun/. electron-builder cannot follow these symlinks
+ * when creating asar archives.
+ *
+ * This script:
+ * 1. Detects if native modules are symlinks
+ * 2. Replaces symlinks with actual file copies
+ * 3. electron-builder can then properly package and unpack them
+ *
+ * This is safe because bun install will recreate the symlinks on next install.
+ */
+
+import { cpSync, existsSync, lstatSync, realpathSync, rmSync } from "node:fs";
+import { dirname, join } from "node:path";
+
+const NATIVE_MODULES = ["node-pty"] as const;
+
+function prepareNativeModules() {
+	console.log("Preparing native modules for electron-builder...");
+
+	const nodeModulesDir = join(dirname(import.meta.dirname), "node_modules");
+
+	for (const moduleName of NATIVE_MODULES) {
+		const modulePath = join(nodeModulesDir, moduleName);
+
+		if (!existsSync(modulePath)) {
+			console.error(`  [ERROR] ${moduleName} not found at ${modulePath}`);
+			process.exit(1);
+		}
+
+		const stats = lstatSync(modulePath);
+
+		if (stats.isSymbolicLink()) {
+			// Resolve symlink to get real path
+			const realPath = realpathSync(modulePath);
+			console.log(`  ${moduleName}: symlink -> replacing with real files`);
+			console.log(`    Real path: ${realPath}`);
+
+			// Remove the symlink
+			rmSync(modulePath);
+
+			// Copy the actual files
+			cpSync(realPath, modulePath, { recursive: true });
+
+			console.log(`    Copied to: ${modulePath}`);
+		} else {
+			console.log(`  ${moduleName}: already real directory (not a symlink)`);
+		}
+	}
+
+	console.log("Done!");
+}
+
+prepareNativeModules();