diff --git a/packages/nuxt/src/auto-imports/transform.ts b/packages/nuxt/src/auto-imports/transform.ts
index de59c98c0e..fb5427c4fd 100644
--- a/packages/nuxt/src/auto-imports/transform.ts
+++ b/packages/nuxt/src/auto-imports/transform.ts
@@ -15,13 +15,8 @@ export const TransformPlugin = createUnplugin(({ ctx, options, sourcemap }: {ctx
       const exclude = options.transform?.exclude || [/[\\/]node_modules[\\/]/]
       const include = options.transform?.include || []
 
-      // Custom includes
-      if (include.some(pattern => id.match(pattern))) {
-        return true
-      }
-
-      // Exclude node_modules by default
-      if (exclude.some(pattern => id.match(pattern))) {
+      // Custom includes - exclude node_modules by default
+      if (exclude.some(pattern => id.match(pattern)) && !include.some(pattern => id.match(pattern))) {
         return false
       }
 
diff --git a/packages/nuxt/src/core/nuxt.ts b/packages/nuxt/src/core/nuxt.ts
index dc184dccff..1a0640b58c 100644
--- a/packages/nuxt/src/core/nuxt.ts
+++ b/packages/nuxt/src/core/nuxt.ts
@@ -143,7 +143,7 @@ export async function loadNuxt (opts: LoadNuxtOptions): Promise<Nuxt> {
   options._modules.push([autoImportsModule, {
     transform: {
       include: options._layers
-        .filter(i => i.cwd)
+        .filter(i => i.cwd && i.cwd.includes('node_modules'))
         .map(i => new RegExp(`(^|\\/)${escapeRE(i.cwd.split('node_modules/').pop())}(\\/|$)(?!node_modules\\/)`))
     }
   }])