diff --git a/scripts/prepare-resources.cjs b/scripts/prepare-resources.cjs
index 1e7924a..9450019 100644
--- a/scripts/prepare-resources.cjs
+++ b/scripts/prepare-resources.cjs
@@ -2,7 +2,8 @@
 const path = require('path');
 
 const projectRoot = path.resolve(__dirname, '..');
-const targetDir = path.resolve(projectRoot, 'src/backend/bundled_resources');
+const backendDir = path.resolve(projectRoot, 'src/backend');
+const resTargetDir = path.resolve(backendDir, 'resources');
 
 function copyRecursiveSync(src, dest) {
     const stats = fs.statSync(src);
@@ -18,31 +19,49 @@
     }
 }
 
-// Ensure target directory exists
-if (fs.existsSync(targetDir)) {
-    fs.rmSync(targetDir, { recursive: true, force: true });
+// Clean and recreate target directories
+if (fs.existsSync(resTargetDir)) {
+    fs.rmSync(resTargetDir, { recursive: true, force: true });
 }
-fs.mkdirSync(targetDir, { recursive: true });
+fs.mkdirSync(resTargetDir, { recursive: true });
 
-// 1. Copy DLLs from bin/ to targetDir (flat)
+// 1. Copy DLLs from bin/ to backend/ (flat) - These go to the APP ROOT in MSI
 const binDir = path.join(projectRoot, 'bin');
 if (fs.existsSync(binDir)) {
     fs.readdirSync(binDir).forEach(file => {
         if (file.endsWith('.dll')) {
             const src = path.join(binDir, file);
-            const dest = path.join(targetDir, file);
+            const dest = path.join(backendDir, file);
             console.log(`Copying ${src} to ${dest}`);
             fs.copyFileSync(src, dest);
         }
     });
 }
 
-// 2. Copy everything from resources/ to targetDir (preserving structure)
-const resDir = path.join(projectRoot, 'resources');
-if (fs.existsSync(resDir)) {
-    fs.readdirSync(resDir).forEach(child => {
-        const src = path.join(resDir, child);
-        const dest = path.join(targetDir, child);
+// 2. Copy critical JSON files from root to resources/
+['mcp.json', 'config.json'].forEach(file => {
+    const src = path.join(projectRoot, file);
+    if (fs.existsSync(src)) {
+        const dest = path.join(resTargetDir, file);
+        console.log(`Copying ${src} to ${dest}`);
+        fs.copyFileSync(src, dest);
+    }
+});
+
+// 3. Copy models/ to resources/models/
+const modelsDir = path.join(projectRoot, 'models');
+if (fs.existsSync(modelsDir)) {
+    const dest = path.join(resTargetDir, 'models');
+    console.log(`Copying ${modelsDir} to ${dest}`);
+    copyRecursiveSync(modelsDir, dest);
+}
+
+// 4. Copy everything from resources/ to backend/resources/ (preserving structure)
+const resSrcDir = path.join(projectRoot, 'resources');
+if (fs.existsSync(resSrcDir)) {
+    fs.readdirSync(resSrcDir).forEach(child => {
+        const src = path.join(resSrcDir, child);
+        const dest = path.join(resTargetDir, child);
         console.log(`Copying ${src} to ${dest}`);
         copyRecursiveSync(src, dest);
     });
diff --git a/src/backend/tauri.conf.json b/src/backend/tauri.conf.json
index ce0fd96..be1ced2 100644
--- a/src/backend/tauri.conf.json
+++ b/src/backend/tauri.conf.json
@@ -28,7 +28,7 @@
     "active": true,
     "targets": "all",
     "externalBin": ["../../bin/llama-server"],
-    "resources": ["bundled_resources/*"],
+    "resources": ["resources/**/*", "*.dll"],
     "icon": [
       "../../resources/icons/32x32.png",
       "../../resources/icons/128x128.png",