diff --git a/packages/vite/src/node/server/moduleGraph.ts b/packages/vite/src/node/server/moduleGraph.ts
index 804e38bc2c3cc7..461c182bb69c55 100644
--- a/packages/vite/src/node/server/moduleGraph.ts
+++ b/packages/vite/src/node/server/moduleGraph.ts
@@ -24,7 +24,8 @@ export class ModuleNode {
   info?: ModuleInfo
   meta?: Record<string, any>
   importers = new Set<ModuleNode>()
-  importedModules = new Set<ModuleNode>()
+  clientImportedModules = new Set<ModuleNode>()
+  ssrImportedModules = new Set<ModuleNode>()
   acceptedHmrDeps = new Set<ModuleNode>()
   acceptedHmrExports: Set<string> | null = null
   importedBindings: Map<string, Set<string>> | null = null
@@ -46,6 +47,14 @@ export class ModuleNode {
       this.isSelfAccepting = false
     }
   }
+
+  get importedModules(): Set<ModuleNode> {
+    const importedModules = new Set(this.clientImportedModules)
+    for (const module of this.ssrImportedModules) {
+      importedModules.add(module)
+    }
+    return importedModules
+  }
 }
 
 export type ResolvedUrl = [
@@ -169,7 +178,7 @@ export class ModuleGraph {
     ssr?: boolean,
   ): Promise<Set<ModuleNode> | undefined> {
     mod.isSelfAccepting = isSelfAccepting
-    const prevImports = mod.importedModules
+    const prevImports = ssr ? mod.ssrImportedModules : mod.clientImportedModules
     let noLongerImported: Set<ModuleNode> | undefined
 
     let resolvePromises = []
@@ -195,11 +204,19 @@ export class ModuleGraph {
       await Promise.all(resolvePromises)
     }
 
-    const nextImports = (mod.importedModules = new Set(resolveResults))
+    const nextImports = new Set(resolveResults)
+    if (ssr) {
+      mod.ssrImportedModules = nextImports
+    } else {
+      mod.clientImportedModules = nextImports
+    }
 
     // remove the importer from deps that were imported but no longer are.
     prevImports.forEach((dep) => {
-      if (!nextImports.has(dep)) {
+      if (
+        !mod.clientImportedModules.has(dep) &&
+        !mod.ssrImportedModules.has(dep)
+      ) {
         dep.importers.delete(mod)
         if (!dep.importers.size) {
           // dependency no longer imported
diff --git a/playground/ssr-deps/__tests__/ssr-deps.spec.ts b/playground/ssr-deps/__tests__/ssr-deps.spec.ts
index a6d8973977e7a3..68d069c5964b94 100644
--- a/playground/ssr-deps/__tests__/ssr-deps.spec.ts
+++ b/playground/ssr-deps/__tests__/ssr-deps.spec.ts
@@ -1,6 +1,6 @@
-import { expect, test } from 'vitest'
+import { describe, expect, test } from 'vitest'
 import { port } from './serve'
-import { getColor, page } from '~utils'
+import { editFile, getColor, isServe, page, untilUpdated } from '~utils'
 
 const url = `http://localhost:${port}`
 
@@ -121,3 +121,46 @@ test('import css library', async () => {
   await page.goto(url)
   expect(await page.textContent('.module-condition')).toMatch('[success]')
 })
+
+test('msg from isomorphic module (server)', async () => {
+  await page.goto(url)
+  expect(await page.textContent('.isomorphic-module-server')).toMatch(
+    '[server]',
+  )
+})
+
+test('msg from isomorphic module (browser)', async () => {
+  await page.goto(url)
+  expect(await page.textContent('.isomorphic-module-browser')).toMatch(
+    '[browser]',
+  )
+})
+
+describe.runIf(isServe)('hmr', () => {
+  test('handle isomorphic module updates', async () => {
+    await page.goto(url)
+
+    expect(await page.textContent('.isomorphic-module-server')).toMatch(
+      '[server]',
+    )
+    expect(await page.textContent('.isomorphic-module-browser')).toMatch(
+      '[browser]',
+    )
+
+    editFile('src/isomorphic-module-browser.js', (code) =>
+      code.replace('[browser]', '[browser-hmr]'),
+    )
+    await page.waitForNavigation()
+    await untilUpdated(async () => {
+      return page.textContent('.isomorphic-module-browser')
+    }, '[browser-hmr]')
+
+    editFile('src/isomorphic-module-server.js', (code) =>
+      code.replace('[server]', '[server-hmr]'),
+    )
+    await page.waitForNavigation()
+    await untilUpdated(async () => {
+      return page.textContent('.isomorphic-module-server')
+    }, '[server-hmr]')
+  })
+})
diff --git a/playground/ssr-deps/index.html b/playground/ssr-deps/index.html
index 72287c441c80b0..45dc6aa35566a2 100644
--- a/playground/ssr-deps/index.html
+++ b/playground/ssr-deps/index.html
@@ -12,5 +12,15 @@ <h1>SSR Dependencies</h1>
       // hydration scripts
       import '@vitejs/test-css-lib'
     </script>
+    <script type="module">
+      // Using dynamic import, so the module is transformed when browser actually
+      // requests it. This essentially disables pre-transform optimization that's
+      // crucial to trigger a race condition, covered by the test case introduced
+      // in https://github.com/vitejs/vite/pull/11973
+      import('virtual:isomorphic-module').then(({ default: message }) => {
+        document.querySelector('.isomorphic-module-browser').textContent =
+          message
+      })
+    </script>
   </body>
 </html>
diff --git a/playground/ssr-deps/server.js b/playground/ssr-deps/server.js
index 3f973a9afec001..05e86a863ea744 100644
--- a/playground/ssr-deps/server.js
+++ b/playground/ssr-deps/server.js
@@ -64,6 +64,23 @@ export async function createServer(root = process.cwd(), hmrPort) {
           }
         },
       },
+      {
+        name: 'virtual-isomorphic-module',
+        resolveId(id) {
+          if (id === 'virtual:isomorphic-module') {
+            return '\0virtual:isomorphic-module'
+          }
+        },
+        load(id, { ssr }) {
+          if (id === '\0virtual:isomorphic-module') {
+            if (ssr) {
+              return 'export { default } from "/src/isomorphic-module-server.js";'
+            } else {
+              return 'export { default } from "/src/isomorphic-module-browser.js";'
+            }
+          }
+        },
+      },
     ],
   })
   // use vite's connect instance as middleware
diff --git a/playground/ssr-deps/src/app.js b/playground/ssr-deps/src/app.js
index 0af57b094d76e0..9942dec47d7401 100644
--- a/playground/ssr-deps/src/app.js
+++ b/playground/ssr-deps/src/app.js
@@ -29,6 +29,7 @@ import optimizedCjsWithNestedExternal from '@vitejs/test-optimized-cjs-with-nest
 import { setMessage } from '@vitejs/test-external-entry/entry'
 setMessage('Hello World!')
 import externalUsingExternalEntry from '@vitejs/test-external-using-external-entry'
+import isomorphicModuleMessage from 'virtual:isomorphic-module'
 
 export async function render(url, rootDir) {
   let html = ''
@@ -90,5 +91,9 @@ export async function render(url, rootDir) {
 
   html += `\n<p class="module-condition">${moduleConditionMessage}</p>`
 
+  html += `\n<p class="isomorphic-module-server">${isomorphicModuleMessage}</p>`
+
+  html += `\n<p class="isomorphic-module-browser"></p>`
+
   return html + '\n'
 }
diff --git a/playground/ssr-deps/src/isomorphic-module-browser.js b/playground/ssr-deps/src/isomorphic-module-browser.js
new file mode 100644
index 00000000000000..95ab03d26f7d7b
--- /dev/null
+++ b/playground/ssr-deps/src/isomorphic-module-browser.js
@@ -0,0 +1,3 @@
+const message = 'message from isomorphic-module (browser): [browser]'
+
+export default message
diff --git a/playground/ssr-deps/src/isomorphic-module-server.js b/playground/ssr-deps/src/isomorphic-module-server.js
new file mode 100644
index 00000000000000..def23eb4caa384
--- /dev/null
+++ b/playground/ssr-deps/src/isomorphic-module-server.js
@@ -0,0 +1,3 @@
+const message = 'message from isomorphic-module (server): [server]'
+
+export default message