diff --git a/docs/guide/cli.md b/docs/guide/cli.md
index faaeefa18cb20f..b80f94da96fe1f 100644
--- a/docs/guide/cli.md
+++ b/docs/guide/cli.md
@@ -79,6 +79,8 @@ vite build [root]
 
 Pre-bundle dependencies.
 
+**Deprecated**: the pre-bundle process runs automatically and does not need to be called.
+
 #### Usage
 
 ```bash
diff --git a/packages/vite/src/node/cli.ts b/packages/vite/src/node/cli.ts
index aeaaafb697b3b3..0b344806975503 100644
--- a/packages/vite/src/node/cli.ts
+++ b/packages/vite/src/node/cli.ts
@@ -333,7 +333,10 @@ cli
 
 // optimize
 cli
-  .command('optimize [root]', 'pre-bundle dependencies')
+  .command(
+    'optimize [root]',
+    'pre-bundle dependencies (deprecated, the pre-bundle process runs automatically and does not need to be called)',
+  )
   .option(
     '--force',
     `[boolean] force the optimizer to ignore the cache and re-bundle`,
diff --git a/packages/vite/src/node/optimizer/index.ts b/packages/vite/src/node/optimizer/index.ts
index 8dcf3da90675af..1951c4ce92d86b 100644
--- a/packages/vite/src/node/optimizer/index.ts
+++ b/packages/vite/src/node/optimizer/index.ts
@@ -246,6 +246,8 @@ export interface DepOptimizationMetadata {
 /**
  * Scan and optimize dependencies within a project.
  * Used by Vite CLI when running `vite optimize`.
+ *
+ * @deprecated the optimization process runs automatically and does not need to be called
  */
 
 export async function optimizeDeps(
@@ -255,6 +257,12 @@ export async function optimizeDeps(
 ): Promise<DepOptimizationMetadata> {
   const log = asCommand ? config.logger.info : debug
 
+  config.logger.warn(
+    colors.yellow(
+      'manually calling optimizeDeps is deprecated. This is done automatically and does not need to be called manually.',
+    ),
+  )
+
   const environment = new ScanEnvironment('client', config)
   await environment.init()