diff --git a/packages/vite/src/node/build.ts b/packages/vite/src/node/build.ts
index 39b3e4fb15acf4..4bc57ce58f76aa 100644
--- a/packages/vite/src/node/build.ts
+++ b/packages/vite/src/node/build.ts
@@ -51,7 +51,11 @@ import { ssrManifestPlugin } from './ssr/ssrManifestPlugin'
 import { loadFallbackPlugin } from './plugins/loadFallback'
 import { findNearestPackageData } from './packages'
 import type { PackageCache } from './packages'
-import { resolveChokidarOptions } from './watch'
+import {
+  getResolvedOutDirs,
+  resolveChokidarOptions,
+  resolveEmptyOutDir,
+} from './watch'
 import { completeSystemWrapPlugin } from './plugins/completeSystemWrap'
 import { mergeConfig } from './publicUtils'
 import { webWorkerPostPlugin } from './plugins/worker'
@@ -655,7 +659,17 @@ export async function build(
       normalizedOutputs.push(buildOutputOptions(outputs))
     }
 
-    const outDirs = normalizedOutputs.map(({ dir }) => resolve(dir!))
+    const resolvedOutDirs = getResolvedOutDirs(
+      config.root,
+      options.outDir,
+      options.rollupOptions?.output,
+    )
+    const emptyOutDir = resolveEmptyOutDir(
+      options.emptyOutDir,
+      config.root,
+      resolvedOutDirs,
+      config.logger,
+    )
 
     // watch file changes with rollup
     if (config.build.watch) {
@@ -664,6 +678,8 @@ export async function build(
       const resolvedChokidarOptions = resolveChokidarOptions(
         config,
         config.build.watch.chokidar,
+        resolvedOutDirs,
+        emptyOutDir,
       )
 
       const { watch } = await import('rollup')
@@ -680,7 +696,7 @@ export async function build(
         if (event.code === 'BUNDLE_START') {
           config.logger.info(colors.cyan(`\nbuild started...`))
           if (options.write) {
-            prepareOutDir(outDirs, options.emptyOutDir, config)
+            prepareOutDir(resolvedOutDirs, emptyOutDir, config)
           }
         } else if (event.code === 'BUNDLE_END') {
           event.result.close()
@@ -699,7 +715,7 @@ export async function build(
     bundle = await rollup(rollupOptions)
 
     if (options.write) {
-      prepareOutDir(outDirs, options.emptyOutDir, config)
+      prepareOutDir(resolvedOutDirs, emptyOutDir, config)
     }
 
     const res: RollupOutput[] = []
@@ -726,36 +742,15 @@ export async function build(
 }
 
 function prepareOutDir(
-  outDirs: string[],
+  outDirs: Set<string>,
   emptyOutDir: boolean | null,
   config: ResolvedConfig,
 ) {
-  const nonDuplicateDirs = new Set(outDirs)
-  let outside = false
-  if (emptyOutDir == null) {
-    for (const outDir of nonDuplicateDirs) {
-      if (
-        fs.existsSync(outDir) &&
-        !normalizePath(outDir).startsWith(withTrailingSlash(config.root))
-      ) {
-        // warn if outDir is outside of root
-        config.logger.warn(
-          colors.yellow(
-            `\n${colors.bold(`(!)`)} outDir ${colors.white(
-              colors.dim(outDir),
-            )} is not inside project root and will not be emptied.\n` +
-              `Use --emptyOutDir to override.\n`,
-          ),
-        )
-        outside = true
-        break
-      }
-    }
-  }
-  for (const outDir of nonDuplicateDirs) {
-    if (!outside && emptyOutDir !== false && fs.existsSync(outDir)) {
+  const outDirsArray = [...outDirs]
+  for (const outDir of outDirs) {
+    if (emptyOutDir !== false && fs.existsSync(outDir)) {
       // skip those other outDirs which are nested in current outDir
-      const skipDirs = outDirs
+      const skipDirs = outDirsArray
         .map((dir) => {
           const relative = path.relative(outDir, dir)
           if (
diff --git a/packages/vite/src/node/server/index.ts b/packages/vite/src/node/server/index.ts
index d36b4c309b3025..c7a73456187938 100644
--- a/packages/vite/src/node/server/index.ts
+++ b/packages/vite/src/node/server/index.ts
@@ -47,7 +47,12 @@ import type { BindCLIShortcutsOptions } from '../shortcuts'
 import { CLIENT_DIR, DEFAULT_DEV_PORT } from '../constants'
 import type { Logger } from '../logger'
 import { printServerUrls } from '../logger'
-import { createNoopWatcher, resolveChokidarOptions } from '../watch'
+import {
+  createNoopWatcher,
+  getResolvedOutDirs,
+  resolveChokidarOptions,
+  resolveEmptyOutDir,
+} from '../watch'
 import { initPublicFiles } from '../publicDir'
 import { getEnvFilesForMode } from '../env'
 import type { FetchResult } from '../../runtime/types'
@@ -428,10 +433,25 @@ export async function _createServer(
   const httpsOptions = await resolveHttpsConfig(config.server.https)
   const { middlewareMode } = serverConfig
 
-  const resolvedWatchOptions = resolveChokidarOptions(config, {
-    disableGlobbing: true,
-    ...serverConfig.watch,
-  })
+  const resolvedOutDirs = getResolvedOutDirs(
+    config.root,
+    config.build.outDir,
+    config.build.rollupOptions?.output,
+  )
+  const emptyOutDir = resolveEmptyOutDir(
+    config.build.emptyOutDir,
+    config.root,
+    resolvedOutDirs,
+  )
+  const resolvedWatchOptions = resolveChokidarOptions(
+    config,
+    {
+      disableGlobbing: true,
+      ...serverConfig.watch,
+    },
+    resolvedOutDirs,
+    emptyOutDir,
+  )
 
   const middlewares = connect() as Connect.Server
   const httpServer = middlewareMode
diff --git a/packages/vite/src/node/watch.ts b/packages/vite/src/node/watch.ts
index 9c9972bdd3a471..d8eb128f1613a5 100644
--- a/packages/vite/src/node/watch.ts
+++ b/packages/vite/src/node/watch.ts
@@ -2,12 +2,58 @@ import { EventEmitter } from 'node:events'
 import path from 'node:path'
 import glob from 'fast-glob'
 import type { FSWatcher, WatchOptions } from 'dep-types/chokidar'
-import { arraify } from './utils'
-import type { ResolvedConfig } from '.'
+import type { OutputOptions } from 'rollup'
+import * as colors from 'picocolors'
+import { withTrailingSlash } from '../shared/utils'
+import { arraify, normalizePath } from './utils'
+import type { ResolvedConfig } from './config'
+import type { Logger } from './logger'
+
+export function getResolvedOutDirs(
+  root: string,
+  outDir: string,
+  outputOptions: OutputOptions[] | OutputOptions | undefined,
+): Set<string> {
+  const resolvedOutDir = path.resolve(root, outDir)
+  if (!outputOptions) return new Set([resolvedOutDir])
+
+  return new Set(
+    arraify(outputOptions).map(({ dir }) =>
+      dir ? path.resolve(root, dir) : resolvedOutDir,
+    ),
+  )
+}
+
+export function resolveEmptyOutDir(
+  emptyOutDir: boolean | null,
+  root: string,
+  outDirs: Set<string>,
+  logger?: Logger,
+): boolean {
+  if (emptyOutDir != null) return emptyOutDir
+
+  for (const outDir of outDirs) {
+    if (!normalizePath(outDir).startsWith(withTrailingSlash(root))) {
+      // warn if outDir is outside of root
+      logger?.warn(
+        colors.yellow(
+          `\n${colors.bold(`(!)`)} outDir ${colors.white(
+            colors.dim(outDir),
+          )} is not inside project root and will not be emptied.\n` +
+            `Use --emptyOutDir to override.\n`,
+        ),
+      )
+      return false
+    }
+  }
+  return true
+}
 
 export function resolveChokidarOptions(
   config: ResolvedConfig,
   options: WatchOptions | undefined,
+  resolvedOutDirs: Set<string>,
+  emptyOutDir: boolean,
 ): WatchOptions {
   const { ignored: ignoredList, ...otherOptions } = options ?? {}
   const ignored: WatchOptions['ignored'] = [
@@ -17,9 +63,9 @@ export function resolveChokidarOptions(
     glob.escapePath(config.cacheDir) + '/**',
     ...arraify(ignoredList || []),
   ]
-  if (config.build.outDir) {
+  if (emptyOutDir) {
     ignored.push(
-      glob.escapePath(path.resolve(config.root, config.build.outDir)) + '/**',
+      ...[...resolvedOutDirs].map((outDir) => glob.escapePath(outDir) + '/**'),
     )
   }