diff --git a/apps/desktop/electron-builder.ts b/apps/desktop/electron-builder.ts
index 68820521693..a58f1210b4c 100644
--- a/apps/desktop/electron-builder.ts
+++ b/apps/desktop/electron-builder.ts
@@ -34,11 +34,24 @@ const config: Configuration = {
 	asar: true,
 	asarUnpack: [
 		"**/node_modules/better-sqlite3/**/*",
+		// better-sqlite3 uses `bindings` to locate native modules - must be unpacked together
+		"**/node_modules/bindings/**/*",
+		"**/node_modules/file-uri-to-path/**/*",
 		"**/node_modules/node-pty/**/*",
 		// Sound files must be unpacked so external audio players (afplay, paplay, etc.) can access them
 		"**/resources/sounds/**/*",
 	],
 
+	// Extra resources placed outside asar archive (accessible via process.resourcesPath)
+	extraResources: [
+		// Database migrations - must be outside asar for drizzle-orm to read
+		{
+			from: "dist/resources/migrations",
+			to: "resources/migrations",
+			filter: ["**/*"],
+		},
+	],
+
 	files: [
 		"dist/**/*",
 		"package.json",
@@ -47,13 +60,8 @@ const config: Configuration = {
 			to: "resources",
 			filter: ["**/*"],
 		},
-		// Database migrations from local-db package (copied to dist/resources/migrations by vite)
-		{
-			from: "dist/resources/migrations",
-			to: "resources/migrations",
-			filter: ["**/*"],
-		},
 		// Native modules that can't be bundled by Vite.
+		// bun creates symlinks for direct deps in workspace node_modules.
 		// The copy:native-modules script replaces symlinks with real files
 		// before building (required for Bun 1.3+ isolated installs).
 		{
@@ -61,6 +69,18 @@ const config: Configuration = {
 			to: "node_modules/better-sqlite3",
 			filter: ["**/*"],
 		},
+		// better-sqlite3 uses `bindings` package to locate its native .node file
+		{
+			from: "node_modules/bindings",
+			to: "node_modules/bindings",
+			filter: ["**/*"],
+		},
+		// `bindings` requires `file-uri-to-path` for file:// URL handling
+		{
+			from: "node_modules/file-uri-to-path",
+			to: "node_modules/file-uri-to-path",
+			filter: ["**/*"],
+		},
 		{
 			from: "node_modules/node-pty",
 			to: "node_modules/node-pty",
@@ -69,10 +89,8 @@ const config: Configuration = {
 		"!**/.DS_Store",
 	],
 
-	// Skip npm rebuild - dependencies already built in monorepo
-	npmRebuild: false,
-	buildDependenciesFromSource: false,
-	nodeGypRebuild: false,
+	// Rebuild native modules for Electron's Node.js version
+	npmRebuild: true,
 
 	// macOS
 	mac: {
diff --git a/apps/desktop/package.json b/apps/desktop/package.json
index 5a3857f4a07..445c4523663 100644
--- a/apps/desktop/package.json
+++ b/apps/desktop/package.json
@@ -59,6 +59,7 @@
 		"@xterm/addon-webgl": "^0.18.0",
 		"@xterm/xterm": "^5.5.0",
 		"better-sqlite3": "12.5.0",
+		"bindings": "^1.5.0",
 		"clsx": "^2.1.1",
 		"culori": "^4.0.2",
 		"date-fns": "^4.1.0",
@@ -71,6 +72,7 @@
 		"execa": "^9.6.0",
 		"express": "^5.1.0",
 		"fast-glob": "^3.3.3",
+		"file-uri-to-path": "^1.0.0",
 		"framer-motion": "^12.23.24",
 		"http-proxy": "^1.18.1",
 		"jose": "^6.1.3",
@@ -79,6 +81,7 @@
 		"lowdb": "^7.0.1",
 		"monaco-editor": "^0.55.1",
 		"nanoid": "^5.1.6",
+		"node-addon-api": "^7.1.0",
 		"node-pty": "1.1.0-beta30",
 		"os-locale": "^6.0.2",
 		"posthog-js": "^1.306.1",
diff --git a/apps/desktop/scripts/copy-native-modules.ts b/apps/desktop/scripts/copy-native-modules.ts
index fc176626c12..0f28a56b4bd 100644
--- a/apps/desktop/scripts/copy-native-modules.ts
+++ b/apps/desktop/scripts/copy-native-modules.ts
@@ -16,42 +16,68 @@
 import { cpSync, existsSync, lstatSync, realpathSync, rmSync } from "node:fs";
 import { dirname, join } from "node:path";
 
+// Native modules that must exist for the app to work
 const NATIVE_MODULES = ["better-sqlite3", "node-pty"] as const;
 
-function prepareNativeModules() {
-	console.log("Preparing native modules for electron-builder...");
+// Dependencies of native modules that need to be copied (may be hoisted or symlinked)
+const NATIVE_MODULE_DEPS = ["bindings", "file-uri-to-path"] as const;
 
-	const nodeModulesDir = join(dirname(import.meta.dirname), "node_modules");
-
-	for (const moduleName of NATIVE_MODULES) {
-		const modulePath = join(nodeModulesDir, moduleName);
+function copyModuleIfSymlink(
+	nodeModulesDir: string,
+	moduleName: string,
+	required: boolean,
+): boolean {
+	const modulePath = join(nodeModulesDir, moduleName);
 
-		if (!existsSync(modulePath)) {
+	if (!existsSync(modulePath)) {
+		if (required) {
 			console.error(`  [ERROR] ${moduleName} not found at ${modulePath}`);
 			process.exit(1);
 		}
+		console.log(`  ${moduleName}: not found (skipping)`);
+		return false;
+	}
 
-		const stats = lstatSync(modulePath);
+	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}`);
+	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);
+		// Remove the symlink
+		rmSync(modulePath);
 
-			// Copy the actual files
-			cpSync(realPath, modulePath, { recursive: true });
+		// 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(`    Copied to: ${modulePath}`);
+	} else {
+		console.log(`  ${moduleName}: already real directory (not a symlink)`);
+	}
+
+	return true;
+}
+
+function prepareNativeModules() {
+	console.log("Preparing native modules for electron-builder...");
+
+	// bun creates symlinks for direct dependencies in the workspace's node_modules
+	const nodeModulesDir = join(dirname(import.meta.dirname), "node_modules");
+
+	// Copy required native modules
+	for (const moduleName of NATIVE_MODULES) {
+		copyModuleIfSymlink(nodeModulesDir, moduleName, true);
+	}
+
+	// Copy native module dependencies (not required but needed if present)
+	console.log("\nPreparing native module dependencies...");
+	for (const moduleName of NATIVE_MODULE_DEPS) {
+		copyModuleIfSymlink(nodeModulesDir, moduleName, false);
 	}
 
-	console.log("Done!");
+	console.log("\nDone!");
 }
 
 prepareNativeModules();
diff --git a/bun.lock b/bun.lock
index 121fd07fe6f..991f0e30f62 100644
--- a/bun.lock
+++ b/bun.lock
@@ -145,6 +145,7 @@
         "@xterm/addon-webgl": "^0.18.0",
         "@xterm/xterm": "^5.5.0",
         "better-sqlite3": "12.5.0",
+        "bindings": "^1.5.0",
         "clsx": "^2.1.1",
         "culori": "^4.0.2",
         "date-fns": "^4.1.0",
@@ -157,6 +158,7 @@
         "execa": "^9.6.0",
         "express": "^5.1.0",
         "fast-glob": "^3.3.3",
+        "file-uri-to-path": "^1.0.0",
         "framer-motion": "^12.23.24",
         "http-proxy": "^1.18.1",
         "jose": "^6.1.3",