diff --git a/packages/vite/src/node/build.ts b/packages/vite/src/node/build.ts
index 3ef16ec019c6d5..fafd460e363d3b 100644
--- a/packages/vite/src/node/build.ts
+++ b/packages/vite/src/node/build.ts
@@ -559,20 +559,22 @@ async function doBuild(
       libOptions,
       config.logger
     )
+    const normalizedOutputs: OutputOptions[] = []
+
+    if (Array.isArray(outputs)) {
+      for (const resolvedOutput of outputs) {
+        normalizedOutputs.push(buildOutputOptions(resolvedOutput))
+      }
+    } else {
+      normalizedOutputs.push(buildOutputOptions(outputs))
+    }
+
+    const outDirs = normalizedOutputs.map(({ dir }) => resolve(dir!))
 
     // watch file changes with rollup
     if (config.build.watch) {
       config.logger.info(colors.cyan(`\nwatching for file changes...`))
 
-      const output: OutputOptions[] = []
-      if (Array.isArray(outputs)) {
-        for (const resolvedOutput of outputs) {
-          output.push(buildOutputOptions(resolvedOutput))
-        }
-      } else {
-        output.push(buildOutputOptions(outputs))
-      }
-
       const resolvedChokidarOptions = resolveChokidarOptions(
         config.build.watch.chokidar
       )
@@ -580,7 +582,7 @@ async function doBuild(
       const { watch } = await import('rollup')
       const watcher = watch({
         ...rollupOptions,
-        output,
+        output: normalizedOutputs,
         watch: {
           ...config.build.watch,
           chokidar: resolvedChokidarOptions
@@ -591,7 +593,7 @@ async function doBuild(
         if (event.code === 'BUNDLE_START') {
           config.logger.info(colors.cyan(`\nbuild started...`))
           if (options.write) {
-            prepareOutDir(outDir, options.emptyOutDir, config)
+            prepareOutDir(outDirs, options.emptyOutDir, config)
           }
         } else if (event.code === 'BUNDLE_END') {
           event.result.close()
@@ -610,24 +612,18 @@ async function doBuild(
     parallelBuilds.push(bundle)
 
     const generate = (output: OutputOptions = {}) => {
-      return bundle[options.write ? 'write' : 'generate'](
-        buildOutputOptions(output)
-      )
+      return bundle[options.write ? 'write' : 'generate'](output)
     }
 
     if (options.write) {
-      prepareOutDir(outDir, options.emptyOutDir, config)
+      prepareOutDir(outDirs, options.emptyOutDir, config)
     }
 
-    if (Array.isArray(outputs)) {
-      const res = []
-      for (const output of outputs) {
-        res.push(await generate(output))
-      }
-      return res
-    } else {
-      return await generate(outputs)
+    const res = []
+    for (const output of normalizedOutputs) {
+      res.push(await generate(output))
     }
+    return Array.isArray(outputs) ? res : res[0]
   } catch (e) {
     outputBuildError(e)
     throw e
@@ -635,30 +631,53 @@ async function doBuild(
 }
 
 function prepareOutDir(
-  outDir: string,
+  outDirs: string[],
   emptyOutDir: boolean | null,
   config: ResolvedConfig
 ) {
-  if (fs.existsSync(outDir)) {
-    if (
-      emptyOutDir == null &&
-      !normalizePath(outDir).startsWith(config.root + '/')
-    ) {
-      // warn if outDir is outside of root
-      config.logger.warn(
-        colors.yellow(
-          `\n${colors.bold(`(!)`)} outDir ${colors.white(
-            colors.dim(outDir)
-          )} is not inside project root and will not be emptied.\n` +
-            `Use --emptyOutDir to override.\n`
+  const nonDuplicateDirs = new Set(outDirs)
+  let outside = false
+  if (emptyOutDir == null) {
+    for (const outDir of nonDuplicateDirs) {
+      if (
+        fs.existsSync(outDir) &&
+        !normalizePath(outDir).startsWith(config.root + '/')
+      ) {
+        // warn if outDir is outside of root
+        config.logger.warn(
+          colors.yellow(
+            `\n${colors.bold(`(!)`)} outDir ${colors.white(
+              colors.dim(outDir)
+            )} is not inside project root and will not be emptied.\n` +
+              `Use --emptyOutDir to override.\n`
+          )
         )
-      )
-    } else if (emptyOutDir !== false) {
-      emptyDir(outDir, ['.git'])
+        outside = true
+        break
+      }
     }
   }
-  if (config.publicDir && fs.existsSync(config.publicDir)) {
-    copyDir(config.publicDir, outDir)
+  for (const outDir of nonDuplicateDirs) {
+    if (!outside && emptyOutDir !== false && fs.existsSync(outDir)) {
+      // skip those other outDirs which are nested in current outDir
+      const skipDirs = outDirs
+        .map((dir) => {
+          const relative = path.relative(outDir, dir)
+          if (
+            relative &&
+            !relative.startsWith('..') &&
+            !path.isAbsolute(relative)
+          ) {
+            return relative
+          }
+          return ''
+        })
+        .filter(Boolean)
+      emptyDir(outDir, [...skipDirs, '.git'])
+    }
+    if (config.publicDir && fs.existsSync(config.publicDir)) {
+      copyDir(config.publicDir, outDir)
+    }
   }
 }
 
diff --git a/packages/vite/src/node/utils.ts b/packages/vite/src/node/utils.ts
index 2c6a8c790c607c..2711a29b7eb703 100644
--- a/packages/vite/src/node/utils.ts
+++ b/packages/vite/src/node/utils.ts
@@ -549,16 +549,45 @@ export function isFileReadable(filename: string): boolean {
   }
 }
 
+const splitFirstDirRE = /(.+?)[\\/](.+)/
+
 /**
  * Delete every file and subdirectory. **The given directory must exist.**
- * Pass an optional `skip` array to preserve files in the root directory.
+ * Pass an optional `skip` array to preserve files under the root directory.
  */
 export function emptyDir(dir: string, skip?: string[]): void {
+  const skipInDir: string[] = []
+  let nested: Map<string, string[]> | null = null
+  if (skip?.length) {
+    for (const file of skip) {
+      if (path.dirname(file) !== '.') {
+        const matched = file.match(splitFirstDirRE)
+        if (matched) {
+          nested ??= new Map()
+          const [, nestedDir, skipPath] = matched
+          let nestedSkip = nested.get(nestedDir)
+          if (!nestedSkip) {
+            nestedSkip = []
+            nested.set(nestedDir, nestedSkip)
+          }
+          if (!nestedSkip.includes(skipPath)) {
+            nestedSkip.push(skipPath)
+          }
+        }
+      } else {
+        skipInDir.push(file)
+      }
+    }
+  }
   for (const file of fs.readdirSync(dir)) {
-    if (skip?.includes(file)) {
+    if (skipInDir.includes(file)) {
       continue
     }
-    fs.rmSync(path.resolve(dir, file), { recursive: true, force: true })
+    if (nested?.has(file)) {
+      emptyDir(path.resolve(dir, file), nested.get(file))
+    } else {
+      fs.rmSync(path.resolve(dir, file), { recursive: true, force: true })
+    }
   }
 }