diff --git a/.changeset/quiet-prerender-root.md b/.changeset/quiet-prerender-root.md
new file mode 100644
index 00000000000..c178e6cd905
--- /dev/null
+++ b/.changeset/quiet-prerender-root.md
@@ -0,0 +1,5 @@
+---
+'@tanstack/start-plugin-core': patch
+---
+
+Resolve the prerender paths against Vite's resolved `root` instead of `process.cwd()`. When the root is not the working directory, `vite build <dir>` and `createBuilder({ root })` previously failed to start the preview server or wrote `index.html`, `pages.json` and `sitemap.xml` outside the project.
diff --git a/packages/start-plugin-core/src/vite/post-server-build.ts b/packages/start-plugin-core/src/vite/post-server-build.ts
index 2e74b7635d1..5ad1b40445e 100644
--- a/packages/start-plugin-core/src/vite/post-server-build.ts
+++ b/packages/start-plugin-core/src/vite/post-server-build.ts
@@ -1,3 +1,4 @@
+import { resolve } from 'pathe'
 import { postBuild } from '../post-build'
 import { getClientOutputDirectory } from './output-directory'
 import { prerenderWithVite } from './prerender'
@@ -15,7 +16,7 @@ export async function postServerBuild({
     startConfig,
     adapter: {
       getClientOutputDirectory() {
-        return getClientOutputDirectory(builder.config)
+        return resolve(builder.config.root, getClientOutputDirectory(builder.config))
       },
       prerender(startConfig) {
         return prerenderWithVite({
diff --git a/packages/start-plugin-core/src/vite/prerender.ts b/packages/start-plugin-core/src/vite/prerender.ts
index 5d1838e43aa..7d2f0eafbca 100644
--- a/packages/start-plugin-core/src/vite/prerender.ts
+++ b/packages/start-plugin-core/src/vite/prerender.ts
@@ -1,3 +1,4 @@
+import { resolve } from 'pathe'
 import { VITE_ENVIRONMENT_NAMES } from '../constants'
 import { prerender } from '../prerender'
 import type { PrerenderHandler } from '../prerender'
@@ -26,7 +27,10 @@ export async function prerenderWithVite({
     )
   }
 
-  const outputDir = clientEnv.config.build.outDir
+  const outputDir = resolve(
+    clientEnv.config.root,
+    clientEnv.config.build.outDir,
+  )
 
   process.env.TSS_PRERENDERING = 'true'
   process.env.TSS_CLIENT_OUTPUT_DIR = outputDir
@@ -66,6 +70,9 @@ async function startPreviewServer(
 
   try {
     return await vite.preview({
+      // Reuse the root the build resolved, so the preview config is not
+      // re-resolved against `process.cwd()` when the root is not the cwd.
+      root: viteConfig.root,
       configFile: viteConfig.configFile,
       preview: {
         port: 0,
diff --git a/packages/start-plugin-core/src/vite/preview-server-plugin/plugin.ts b/packages/start-plugin-core/src/vite/preview-server-plugin/plugin.ts
index 1541d9edfbe..d9c815b855b 100644
--- a/packages/start-plugin-core/src/vite/preview-server-plugin/plugin.ts
+++ b/packages/start-plugin-core/src/vite/preview-server-plugin/plugin.ts
@@ -1,5 +1,5 @@
 import { pathToFileURL } from 'node:url'
-import { basename, extname, join } from 'pathe'
+import { basename, extname, join, resolve } from 'pathe'
 import { NodeRequest, sendNodeResponse } from 'srvx/node'
 import { joinURL } from 'ufo'
 import { VITE_ENVIRONMENT_NAMES } from '../../constants'
@@ -36,7 +36,10 @@ export function previewServerPlugin(): Plugin {
 
                 // Get basename without extension and add .js
                 const outputFilename = `${basename(serverInput, extname(serverInput))}.js`
-                const serverOutputDir = getServerOutputDirectory(server.config)
+                const serverOutputDir = resolve(
+                  server.config.root,
+                  getServerOutputDirectory(server.config),
+                )
                 const serverEntryPath = join(serverOutputDir, outputFilename)
                 const imported = await import(
                   pathToFileURL(serverEntryPath).toString()
diff --git a/packages/start-plugin-core/tests/prerender-vite.test.ts b/packages/start-plugin-core/tests/prerender-vite.test.ts
index 013557e4dfa..12fb0fc12fe 100644
--- a/packages/start-plugin-core/tests/prerender-vite.test.ts
+++ b/packages/start-plugin-core/tests/prerender-vite.test.ts
@@ -122,4 +122,31 @@ describe('Vite prerender network sink', () => {
       'http://127.0.0.1:4173/next/?from=about',
     ])
   })
+
+  it('resolves the client output directory and the preview root against the Vite root', async () => {
+    vi.stubGlobal(
+      'fetch',
+      vi.fn(async () => new Response(null, { status: 200 })),
+    )
+    const builder = {
+      environments: {
+        ssr: {
+          config: { root: '/repo/project', configFile: '/vite.config.ts' },
+        },
+        client: {
+          config: { root: '/repo/project', build: { outDir: 'dist/client' } },
+        },
+      },
+    } as any
+
+    await prerenderWithVite({
+      startConfig: { ...makeStartConfig(), pages: [] },
+      builder,
+    })
+
+    expect(preview).toHaveBeenCalledWith(
+      expect.objectContaining({ root: '/repo/project' }),
+    )
+    expect(process.env.TSS_CLIENT_OUTPUT_DIR).toBe('/repo/project/dist/client')
+  })
 })