diff --git a/docs/2.guide/2.directory-structure/1.plugins.md b/docs/2.guide/2.directory-structure/1.plugins.md
index 85ebd33b4..544b7dec9 100644
--- a/docs/2.guide/2.directory-structure/1.plugins.md
+++ b/docs/2.guide/2.directory-structure/1.plugins.md
@@ -21,14 +21,14 @@ For example:
 
 ```bash
 plugins
- | - myPlugin.ts
+ | - myPlugin.ts  // scanned
  | - myOtherPlugin
- | --- supportingFile.ts
- | --- componentToRegister.vue
- | --- index.ts
+ | --- supportingFile.ts   // not scanned
+ | --- componentToRegister.vue   // not scanned
+ | --- index.ts  // currently scanned but deprecated
 ```
 
-Only `myPlugin.ts` and `myOtherPlugin/index.ts` would be registered.
+Only `myPlugin.ts` and `myOtherPlugin/index.ts` would be registered. You can configure [`plugins`](/docs/api/configuration/nuxt-config#plugins-1) to include unscanned files.
 
 ## Creating Plugins
 
diff --git a/packages/kit/src/plugin.ts b/packages/kit/src/plugin.ts
index a15b55b0c..89929c9be 100644
--- a/packages/kit/src/plugin.ts
+++ b/packages/kit/src/plugin.ts
@@ -19,6 +19,12 @@ export function normalizePlugin (plugin: NuxtPlugin | string): NuxtPlugin {
     throw new Error('Invalid plugin. src option is required: ' + JSON.stringify(plugin))
   }
 
+  // TODO: only scan top-level files #18418
+  const nonTopLevelPlugin = plugin.src.match(/\/plugins\/[^/]+\/index\.[^/]+$/i)
+  if (nonTopLevelPlugin && nonTopLevelPlugin.length > 0 && !useNuxt().options.plugins.find(i => (typeof i === 'string' ? i : i.src).endsWith(nonTopLevelPlugin[0]))) {
+    console.warn(`[warn] [nuxt] [deprecation] You are using a plugin that is within a subfolder of your plugins directory without adding it to your config explicitly. You can move it to the top-level plugins directory, or include the file '~${nonTopLevelPlugin[0]}' in your plugins config (https://nuxt.com/docs/api/configuration/nuxt-config#plugins-1) to remove this warning.`)
+  }
+
   // Normalize full path to plugin
   plugin.src = normalize(resolveAlias(plugin.src))
 
diff --git a/packages/nuxt/src/core/app.ts b/packages/nuxt/src/core/app.ts
index fc0ce984b..32a3b10f7 100644
--- a/packages/nuxt/src/core/app.ts
+++ b/packages/nuxt/src/core/app.ts
@@ -112,7 +112,7 @@ export async function resolveApp (nuxt: Nuxt, app: NuxtApp) {
       ...config.srcDir
         ? await resolveFiles(config.srcDir, [
           `${config.dir?.plugins || 'plugins'}/*.{ts,js,mjs,cjs,mts,cts}`,
-          `${config.dir?.plugins || 'plugins'}/*/index.*{ts,js,mjs,cjs,mts,cts}`
+          `${config.dir?.plugins || 'plugins'}/*/index.*{ts,js,mjs,cjs,mts,cts}` // TODO: remove, only scan top-level plugins #18418
         ])
         : []
     ].map(plugin => normalizePlugin(plugin as NuxtPlugin)))