diff --git a/packages/vite/src/node/__tests__/build.spec.ts b/packages/vite/src/node/__tests__/build.spec.ts
index d0a9750763c055..f36811178cc238 100644
--- a/packages/vite/src/node/__tests__/build.spec.ts
+++ b/packages/vite/src/node/__tests__/build.spec.ts
@@ -1,6 +1,7 @@
 import { basename, resolve } from 'node:path'
 import { fileURLToPath } from 'node:url'
 import { stripVTControlCharacters } from 'node:util'
+import fsp from 'node:fs/promises'
 import colors from 'picocolors'
 import { afterEach, describe, expect, test, vi } from 'vitest'
 import type {
@@ -1037,6 +1038,62 @@ describe('onRollupLog', () => {
   )
 })
 
+test('watch rebuild manifest', async (ctx) => {
+  // this doesn't actually test watch rebuild
+  // but it simulates something similar by running two builds for the same environment
+  const root = resolve(__dirname, 'fixtures/watch-rebuild-manifest')
+  const builder = await createBuilder({
+    root,
+    logLevel: 'error',
+    environments: {
+      client: {
+        build: {
+          rollupOptions: {
+            input: '/entry.js',
+          },
+        },
+      },
+    },
+    build: {
+      manifest: true,
+    },
+  })
+
+  function getManifestKeys(output: RollupOutput) {
+    return Object.keys(
+      JSON.parse(
+        (output.output.find((o) => o.fileName === '.vite/manifest.json') as any)
+          .source,
+      ),
+    )
+  }
+
+  const result = await builder.build(builder.environments.client)
+  expect(getManifestKeys(result as RollupOutput)).toMatchInlineSnapshot(`
+    [
+      "dep.js",
+      "entry.js",
+    ]
+  `)
+
+  const entry = resolve(root, 'entry.js')
+  const content = await fsp.readFile(entry, 'utf-8')
+  await fsp.writeFile(
+    entry,
+    content.replace(`import('./dep.js')`, `'dep.js removed'`),
+  )
+  ctx.onTestFinished(async () => {
+    await fsp.writeFile(entry, content)
+  })
+
+  const result2 = await builder.build(builder.environments.client)
+  expect(getManifestKeys(result2 as RollupOutput)).toMatchInlineSnapshot(`
+    [
+      "entry.js",
+    ]
+  `)
+})
+
 /**
  * for each chunks in output1, if there's a chunk in output2 with the same fileName,
  * ensure that the chunk code is the same. if not, the chunk hash should have changed.
diff --git a/packages/vite/src/node/__tests__/fixtures/watch-rebuild-manifest/dep.js b/packages/vite/src/node/__tests__/fixtures/watch-rebuild-manifest/dep.js
new file mode 100644
index 00000000000000..b2d751bb9596b9
--- /dev/null
+++ b/packages/vite/src/node/__tests__/fixtures/watch-rebuild-manifest/dep.js
@@ -0,0 +1 @@
+console.log('dep.js')
diff --git a/packages/vite/src/node/__tests__/fixtures/watch-rebuild-manifest/entry.js b/packages/vite/src/node/__tests__/fixtures/watch-rebuild-manifest/entry.js
new file mode 100644
index 00000000000000..518e2ea9f42ffa
--- /dev/null
+++ b/packages/vite/src/node/__tests__/fixtures/watch-rebuild-manifest/entry.js
@@ -0,0 +1,2 @@
+console.log('entry.js')
+console.log(import('./dep.js'))
diff --git a/packages/vite/src/node/__tests__/fixtures/watch-rebuild-manifest/package.json b/packages/vite/src/node/__tests__/fixtures/watch-rebuild-manifest/package.json
new file mode 100644
index 00000000000000..3dbc1ca591c055
--- /dev/null
+++ b/packages/vite/src/node/__tests__/fixtures/watch-rebuild-manifest/package.json
@@ -0,0 +1,3 @@
+{
+  "type": "module"
+}
diff --git a/packages/vite/src/node/plugins/manifest.ts b/packages/vite/src/node/plugins/manifest.ts
index ea58d16a21903f..52b99cf9bc0b81 100644
--- a/packages/vite/src/node/plugins/manifest.ts
+++ b/packages/vite/src/node/plugins/manifest.ts
@@ -32,6 +32,7 @@ export function manifestPlugin(): Plugin {
       manifest: {} as Manifest,
       outputCount: 0,
       reset() {
+        this.manifest = {}
         this.outputCount = 0
       },
     }
diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml
index 0d05316c53ed72..a256a473394a1a 100644
--- a/pnpm-lock.yaml
+++ b/pnpm-lock.yaml
@@ -436,6 +436,8 @@ importers:
 
   packages/vite/src/node/__tests__/fixtures/test-dep-conditions: {}
 
+  packages/vite/src/node/__tests__/fixtures/watch-rebuild-manifest: {}
+
   packages/vite/src/node/__tests__/packages: {}
 
   packages/vite/src/node/__tests__/packages/child: {}