diff --git a/packages/vite/src/node/plugins/css.ts b/packages/vite/src/node/plugins/css.ts
index 2333a721df8d4f..872bb14168a245 100644
--- a/packages/vite/src/node/plugins/css.ts
+++ b/packages/vite/src/node/plugins/css.ts
@@ -606,11 +606,12 @@ export function cssPostPlugin(config: ResolvedConfig): Plugin {
       }
 
       if (config.build.cssCodeSplit) {
-        if (isPureCssChunk) {
-          // this is a shared CSS-only chunk that is empty.
-          pureCssChunks.add(chunk)
-        }
         if (opts.format === 'es' || opts.format === 'cjs') {
+          if (isPureCssChunk) {
+            // this is a shared CSS-only chunk that is empty.
+            pureCssChunks.add(chunk)
+          }
+
           const isEntry = chunk.isEntry && isPureCssChunk
           const cssAssetName = ensureFileExt(chunk.name, '.css')
           const originalFilename = getChunkOriginalFileName(
diff --git a/packages/vite/src/node/plugins/manifest.ts b/packages/vite/src/node/plugins/manifest.ts
index eff3212d2fc06c..d01a959efca5fa 100644
--- a/packages/vite/src/node/plugins/manifest.ts
+++ b/packages/vite/src/node/plugins/manifest.ts
@@ -111,8 +111,14 @@ export function manifestPlugin(config: ResolvedConfig): Plugin {
       const fileNameToAssetMeta = new Map<string, GeneratedAssetMeta>()
       const assets = generatedAssets.get(config)!
       assets.forEach((asset, referenceId) => {
-        const fileName = this.getFileName(referenceId)
-        fileNameToAssetMeta.set(fileName, asset)
+        try {
+          const fileName = this.getFileName(referenceId)
+          fileNameToAssetMeta.set(fileName, asset)
+        } catch (error: unknown) {
+          // The asset was generated as part of a different output option.
+          // It was already handled during the previous run of this plugin.
+          assets.delete(referenceId)
+        }
       })
 
       const fileNameToAsset = new Map<string, ManifestChunk>()
diff --git a/playground/legacy/__tests__/watch/styles-only-entry-watch.spec.ts b/playground/legacy/__tests__/watch/styles-only-entry-watch.spec.ts
new file mode 100644
index 00000000000000..7fd7f9391316fa
--- /dev/null
+++ b/playground/legacy/__tests__/watch/styles-only-entry-watch.spec.ts
@@ -0,0 +1,47 @@
+import { expect, test } from 'vitest'
+import {
+  editFile,
+  findAssetFile,
+  isBuild,
+  notifyRebuildComplete,
+  readManifest,
+  watcher,
+} from '~utils'
+
+test.runIf(isBuild)('rebuilds styles only entry on change', async () => {
+  expect(findAssetFile(/style-only-entry-.+\.css/, 'watch')).toContain(
+    'hotpink',
+  )
+  expect(findAssetFile(/style-only-entry-legacy-.+\.js/, 'watch')).toContain(
+    'hotpink',
+  )
+  expect(findAssetFile(/polyfills-legacy-.+\.js/, 'watch')).toBeTruthy()
+  const numberOfManifestEntries = Object.keys(readManifest('watch')).length
+  expect(numberOfManifestEntries).toBe(3)
+
+  editFile(
+    'style-only-entry.css',
+    (originalContents) => originalContents.replace('hotpink', 'lightpink'),
+    true,
+  )
+  await notifyRebuildComplete(watcher)
+
+  const updatedManifest = readManifest('watch')
+  expect(Object.keys(updatedManifest)).toHaveLength(numberOfManifestEntries)
+
+  // We must use the file referenced in the manifest here,
+  // since there'll be different versions of the file with different hashes.
+  const reRenderedCssFile = findAssetFile(
+    updatedManifest['style-only-entry.css']!.file.substring('assets/'.length),
+    'watch',
+  )
+  expect(reRenderedCssFile).toContain('lightpink')
+  const reRenderedCssLegacyFile = findAssetFile(
+    updatedManifest['style-only-entry-legacy.css']!.file.substring(
+      'assets/'.length,
+    ),
+    'watch',
+  )
+  expect(reRenderedCssLegacyFile).toContain('lightpink')
+  expect(findAssetFile(/polyfills-legacy-.+\.js/, 'watch')).toBeTruthy()
+})
diff --git a/playground/legacy/package.json b/playground/legacy/package.json
index 542fe20286f04a..85c9c72a3f960f 100644
--- a/playground/legacy/package.json
+++ b/playground/legacy/package.json
@@ -10,6 +10,7 @@
     "build:multiple-output": "vite --config ./vite.config-multiple-output.js build",
     "build:no-polyfills": "vite --config ./vite.config-no-polyfills.js build",
     "build:no-polyfills-no-systemjs": "vite --config ./vite.config-no-polyfills-no-systemjs.js build",
+    "build:watch": "vite --config ./vite.config-watch.js build --debug legacy",
     "debug": "node --inspect-brk ../../packages/vite/bin/vite",
     "preview": "vite preview"
   },
diff --git a/playground/legacy/style-only-entry.css b/playground/legacy/style-only-entry.css
new file mode 100644
index 00000000000000..d88f88426437a3
--- /dev/null
+++ b/playground/legacy/style-only-entry.css
@@ -0,0 +1,3 @@
+:root {
+  background: hotpink;
+}
diff --git a/playground/legacy/vite.config-watch.js b/playground/legacy/vite.config-watch.js
new file mode 100644
index 00000000000000..48d57f3e988edc
--- /dev/null
+++ b/playground/legacy/vite.config-watch.js
@@ -0,0 +1,17 @@
+import { resolve } from 'node:path'
+import legacy from '@vitejs/plugin-legacy'
+import { defineConfig } from 'vite'
+
+export default defineConfig({
+  plugins: [legacy()],
+  build: {
+    manifest: true,
+    rollupOptions: {
+      input: {
+        'style-only-entry': resolve(__dirname, 'style-only-entry.css'),
+      },
+    },
+    watch: {},
+    outDir: 'dist/watch',
+  },
+})