diff --git a/.changeset/fresh-ducks-hydrate.md b/.changeset/fresh-ducks-hydrate.md
new file mode 100644
index 0000000000..27c897932d
--- /dev/null
+++ b/.changeset/fresh-ducks-hydrate.md
@@ -0,0 +1,5 @@
+---
+'@tanstack/react-router': patch
+---
+
+Avoid wrapping root components that may render the HTML document in a Suspense boundary during SSR and hydration.
diff --git a/e2e/react-start/root-document-hydration/.gitignore b/e2e/react-start/root-document-hydration/.gitignore
new file mode 100644
index 0000000000..229709a89d
--- /dev/null
+++ b/e2e/react-start/root-document-hydration/.gitignore
@@ -0,0 +1,5 @@
+node_modules
+dist
+test-results
+playwright-report
+port*.txt
diff --git a/e2e/react-start/root-document-hydration/.prettierignore b/e2e/react-start/root-document-hydration/.prettierignore
new file mode 100644
index 0000000000..083bdb7c4c
--- /dev/null
+++ b/e2e/react-start/root-document-hydration/.prettierignore
@@ -0,0 +1 @@
+src/routeTree.gen.ts
diff --git a/e2e/react-start/root-document-hydration/package.json b/e2e/react-start/root-document-hydration/package.json
new file mode 100644
index 0000000000..d69ddfc0bf
--- /dev/null
+++ b/e2e/react-start/root-document-hydration/package.json
@@ -0,0 +1,40 @@
+{
+  "name": "tanstack-react-start-e2e-root-document-hydration",
+  "private": true,
+  "sideEffects": false,
+  "type": "module",
+  "scripts": {
+    "dev": "vite dev --port 3000",
+    "dev:e2e": "vite dev --port $PORT",
+    "build": "vite build && tsc --noEmit",
+    "start": "pnpx srvx --prod -s ../client dist/server/server.js",
+    "test:e2e:dev": "MODE=dev playwright test --project=chromium",
+    "test:e2e:prod": "MODE=prod playwright test --project=chromium",
+    "test:e2e": "rm -rf port*.txt; pnpm run test:e2e:dev && pnpm run test:e2e:prod"
+  },
+  "dependencies": {
+    "@tanstack/react-router": "workspace:*",
+    "@tanstack/react-start": "workspace:*",
+    "react": "^19.0.0",
+    "react-dom": "^19.0.0"
+  },
+  "devDependencies": {
+    "@playwright/test": "^1.61.0",
+    "@tanstack/router-e2e-utils": "workspace:*",
+    "@types/node": "^22.10.2",
+    "@types/react": "^19.0.8",
+    "@types/react-dom": "^19.0.3",
+    "@vitejs/plugin-react": "^6.0.1",
+    "srvx": "^0.11.9",
+    "@typescript/native": "npm:typescript@^7.0.2",
+    "typescript": "npm:@typescript/typescript6@^6.0.2",
+    "vite": "^8.0.14"
+  },
+  "nx": {
+    "targets": {
+      "test:e2e": {
+        "parallelism": false
+      }
+    }
+  }
+}
diff --git a/e2e/react-start/root-document-hydration/playwright.config.ts b/e2e/react-start/root-document-hydration/playwright.config.ts
new file mode 100644
index 0000000000..18abea0ab1
--- /dev/null
+++ b/e2e/react-start/root-document-hydration/playwright.config.ts
@@ -0,0 +1,36 @@
+import { defineConfig, devices } from '@playwright/test'
+import { getTestServerPort } from '@tanstack/router-e2e-utils'
+import packageJson from './package.json' with { type: 'json' }
+
+const isDev = process.env.MODE === 'dev'
+const PORT = await getTestServerPort(packageJson.name)
+const baseURL = `http://localhost:${PORT}`
+
+export default defineConfig({
+  testDir: './tests',
+  workers: 1,
+  reporter: [['line']],
+
+  use: {
+    baseURL,
+  },
+
+  webServer: {
+    command: isDev ? 'pnpm dev:e2e' : `pnpm build && PORT=${PORT} pnpm start`,
+    url: baseURL,
+    reuseExistingServer: !process.env.CI,
+    stdout: 'pipe',
+    env: {
+      PORT: String(PORT),
+    },
+  },
+
+  projects: [
+    {
+      name: 'chromium',
+      use: {
+        ...devices['Desktop Chrome'],
+      },
+    },
+  ],
+})
diff --git a/e2e/react-start/root-document-hydration/src/routeTree.gen.ts b/e2e/react-start/root-document-hydration/src/routeTree.gen.ts
new file mode 100644
index 0000000000..dceedffdc1
--- /dev/null
+++ b/e2e/react-start/root-document-hydration/src/routeTree.gen.ts
@@ -0,0 +1,68 @@
+/* eslint-disable */
+
+// @ts-nocheck
+
+// noinspection JSUnusedGlobalSymbols
+
+// This file was automatically generated by TanStack Router.
+// You should NOT make any changes in this file as it will be overwritten.
+// Additionally, you should also exclude this file from your linter and/or formatter to prevent it from being checked or modified.
+
+import { Route as rootRouteImport } from './routes/__root'
+import { Route as IndexRouteImport } from './routes/index'
+
+const IndexRoute = IndexRouteImport.update({
+  id: '/',
+  path: '/',
+  getParentRoute: () => rootRouteImport,
+} as any)
+
+export interface FileRoutesByFullPath {
+  '/': typeof IndexRoute
+}
+export interface FileRoutesByTo {
+  '/': typeof IndexRoute
+}
+export interface FileRoutesById {
+  __root__: typeof rootRouteImport
+  '/': typeof IndexRoute
+}
+export interface FileRouteTypes {
+  fileRoutesByFullPath: FileRoutesByFullPath
+  fullPaths: '/'
+  fileRoutesByTo: FileRoutesByTo
+  to: '/'
+  id: '__root__' | '/'
+  fileRoutesById: FileRoutesById
+}
+export interface RootRouteChildren {
+  IndexRoute: typeof IndexRoute
+}
+
+declare module '@tanstack/react-router' {
+  interface FileRoutesByPath {
+    '/': {
+      id: '/'
+      path: '/'
+      fullPath: '/'
+      preLoaderRoute: typeof IndexRouteImport
+      parentRoute: typeof rootRouteImport
+    }
+  }
+}
+
+const rootRouteChildren: RootRouteChildren = {
+  IndexRoute: IndexRoute,
+}
+export const routeTree = rootRouteImport
+  ._addFileChildren(rootRouteChildren)
+  ._addFileTypes<FileRouteTypes>()
+
+import type { getRouter } from './router.tsx'
+import type { createStart } from '@tanstack/react-start'
+declare module '@tanstack/react-start' {
+  interface Register {
+    ssr: true
+    router: Awaited<ReturnType<typeof getRouter>>
+  }
+}
diff --git a/e2e/react-start/root-document-hydration/src/router.tsx b/e2e/react-start/root-document-hydration/src/router.tsx
new file mode 100644
index 0000000000..58f4d54e88
--- /dev/null
+++ b/e2e/react-start/root-document-hydration/src/router.tsx
@@ -0,0 +1,6 @@
+import { createRouter } from '@tanstack/react-router'
+import { routeTree } from './routeTree.gen'
+
+export function getRouter() {
+  return createRouter({ routeTree })
+}
diff --git a/e2e/react-start/root-document-hydration/src/routes/__root.tsx b/e2e/react-start/root-document-hydration/src/routes/__root.tsx
new file mode 100644
index 0000000000..2dc235e951
--- /dev/null
+++ b/e2e/react-start/root-document-hydration/src/routes/__root.tsx
@@ -0,0 +1,36 @@
+import {
+  HeadContent,
+  Outlet,
+  Scripts,
+  createRootRoute,
+} from '@tanstack/react-router'
+import { useEffect } from 'react'
+
+export const Route = createRootRoute({
+  pendingComponent: () => null,
+  component: RootComponent,
+})
+
+function RootComponent() {
+  useEffect(() => {
+    document.documentElement.dataset.hydrated = 'true'
+  }, [])
+
+  return (
+    <html>
+      <head>
+        <HeadContent />
+      </head>
+      <body>
+        <div data-testid="ssr-node" />
+        <script
+          dangerouslySetInnerHTML={{
+            __html: `window.__ssrNode ??= document.currentScript.previousElementSibling`,
+          }}
+        />
+        <Outlet />
+        <Scripts />
+      </body>
+    </html>
+  )
+}
diff --git a/e2e/react-start/root-document-hydration/src/routes/index.tsx b/e2e/react-start/root-document-hydration/src/routes/index.tsx
new file mode 100644
index 0000000000..175d56fb03
--- /dev/null
+++ b/e2e/react-start/root-document-hydration/src/routes/index.tsx
@@ -0,0 +1,5 @@
+import { createFileRoute } from '@tanstack/react-router'
+
+export const Route = createFileRoute('/')({
+  component: () => <main>Root document hydration</main>,
+})
diff --git a/e2e/react-start/root-document-hydration/tests/root-document-hydration.spec.ts b/e2e/react-start/root-document-hydration/tests/root-document-hydration.spec.ts
new file mode 100644
index 0000000000..185fe63dba
--- /dev/null
+++ b/e2e/react-start/root-document-hydration/tests/root-document-hydration.spec.ts
@@ -0,0 +1,47 @@
+import { expect } from '@playwright/test'
+import { test } from '@tanstack/router-e2e-utils'
+
+test('a root pendingComponent preserves the SSR document during hydration', async ({
+  page,
+}) => {
+  await page.addInitScript(() => {
+    const state = { removed: false }
+    ;(window as any).__hydration = state
+
+    new MutationObserver((records) => {
+      const ssrNode = (window as any).__ssrNode as Node | undefined
+      if (!ssrNode) {
+        return
+      }
+
+      for (const record of records) {
+        for (const removedNode of record.removedNodes) {
+          if (
+            removedNode === ssrNode ||
+            (removedNode instanceof Element && removedNode.contains(ssrNode))
+          ) {
+            state.removed = true
+          }
+        }
+      }
+    }).observe(document, { childList: true, subtree: true })
+  })
+
+  const response = await page.goto('/')
+  expect(response?.ok()).toBe(true)
+  await expect(page.locator('html')).toHaveAttribute('data-hydrated', 'true')
+
+  expect(
+    await page.evaluate(() => ({
+      captured: !!(window as any).__ssrNode,
+      removed: (window as any).__hydration.removed,
+      replaced:
+        (window as any).__ssrNode !==
+        document.querySelector('[data-testid="ssr-node"]'),
+    })),
+  ).toEqual({
+    captured: true,
+    removed: false,
+    replaced: false,
+  })
+})
diff --git a/e2e/react-start/root-document-hydration/tsconfig.json b/e2e/react-start/root-document-hydration/tsconfig.json
new file mode 100644
index 0000000000..2afe40d931
--- /dev/null
+++ b/e2e/react-start/root-document-hydration/tsconfig.json
@@ -0,0 +1,18 @@
+{
+  "include": ["**/*.ts", "**/*.tsx"],
+  "compilerOptions": {
+    "strict": true,
+    "esModuleInterop": true,
+    "jsx": "react-jsx",
+    "module": "ESNext",
+    "moduleResolution": "Bundler",
+    "lib": ["DOM", "DOM.Iterable", "ES2022"],
+    "isolatedModules": true,
+    "resolveJsonModule": true,
+    "skipLibCheck": true,
+    "target": "ES2022",
+    "allowJs": true,
+    "forceConsistentCasingInFileNames": true,
+    "noEmit": true
+  }
+}
diff --git a/e2e/react-start/root-document-hydration/vite.config.ts b/e2e/react-start/root-document-hydration/vite.config.ts
new file mode 100644
index 0000000000..c32652e9c8
--- /dev/null
+++ b/e2e/react-start/root-document-hydration/vite.config.ts
@@ -0,0 +1,11 @@
+import { defineConfig } from 'vite'
+import { tanstackStart } from '@tanstack/react-start/plugin/vite'
+import viteReact from '@vitejs/plugin-react'
+
+export default defineConfig({
+  resolve: { tsconfigPaths: true },
+  server: {
+    port: 3000,
+  },
+  plugins: [tanstackStart(), viteReact()],
+})
diff --git a/packages/react-router/src/Match.tsx b/packages/react-router/src/Match.tsx
index 922c0aa588..a0bfa89d55 100644
--- a/packages/react-router/src/Match.tsx
+++ b/packages/react-router/src/Match.tsx
@@ -48,6 +48,18 @@ const outletMatchSelectionEqual = (
   b: OutletMatchSelection,
 ) => a[0] === b[0] && a[1] === b[1]
 
+const canWrapInSuspense = (
+  router: ReturnType<typeof useRouter>,
+  route: AnyRoute,
+  ssr: AnyRouteMatch['ssr'],
+) =>
+  !route.isRoot ||
+  (route.options as RootRouteOptions).shellComponent ||
+  route.options.wrapInSuspense ||
+  ssr === false ||
+  ssr === 'data-only' ||
+  !((isServer ?? router.isServer) || router.ssr)
+
 export const Match = React.memo(function MatchImpl({
   routeId,
 }: {
@@ -89,10 +101,13 @@ function MatchView({
     : route.options.notFoundComponent
 
   const resolvedNoSsr = match.ssr === false || match.ssr === 'data-only'
+  // A root component may render the document itself. Only place its Suspense
+  // boundary in pure CSR, inside an explicit shell, or when explicitly opted in.
   const ResolvedSuspenseBoundary =
+    canWrapInSuspense(router, route, match.ssr) &&
     (route.options.wrapInSuspense ??
-    pendingElement ??
-    ((route.options.errorComponent as any)?.preload || resolvedNoSsr))
+      pendingElement ??
+      ((route.options.errorComponent as any)?.preload || resolvedNoSsr))
       ? React.Suspense
       : SafeFragment
 
@@ -198,6 +213,11 @@ export const MatchInner = React.memo(function MatchInnerImpl({
   }, [key, route.options.component, router.options.defaultComponent])
 
   if (match.status === 'pending') {
+    if (router.ssr && !canWrapInSuspense(router, route, match.ssr)) {
+      // Replacing an SSR document root with pending UI would remove <html>.
+      // Hydrated matches retain their prior data, so keep rendering it.
+      return out
+    }
     if (router._tx) {
       throw router._tx[5]
     }
diff --git a/packages/react-router/tests/root-pending-min.test.tsx b/packages/react-router/tests/root-pending-min.test.tsx
index 0216ae4fec..1ce8ab4822 100644
--- a/packages/react-router/tests/root-pending-min.test.tsx
+++ b/packages/react-router/tests/root-pending-min.test.tsx
@@ -84,8 +84,8 @@ test('a post-hydration root reload keeps its fallback through pendingMinMs', asy
   })
 
   expect(rootLoader).toHaveBeenCalledTimes(1)
-  expect(screen.getByTestId('root-pending')).toBeInTheDocument()
-  expect(screen.getByTestId('root-content')).not.toBeVisible()
+  expect(screen.queryByTestId('root-pending')).not.toBeInTheDocument()
+  expect(screen.getByTestId('root-content')).toHaveTextContent('Generation 1')
 
   await act(async () => {
     reloadGate.resolve()
@@ -95,7 +95,7 @@ test('a post-hydration root reload keeps its fallback through pendingMinMs', asy
   await act(async () => {
     await vi.advanceTimersByTimeAsync(99)
   })
-  expect(screen.getByTestId('root-pending')).toBeInTheDocument()
+  expect(screen.queryByTestId('root-pending')).not.toBeInTheDocument()
 
   await act(async () => {
     await vi.advanceTimersByTimeAsync(1)
@@ -105,7 +105,7 @@ test('a post-hydration root reload keeps its fallback through pendingMinMs', asy
   expect(screen.getByTestId('root-content')).toHaveTextContent('Generation 2')
 })
 
-test('root route hydration preserves component state across its Suspense boundary', async () => {
+test('root route hydration without a pending boundary preserves component state', async () => {
   const mounts = vi.fn()
   const unmounts = vi.fn()
   const initializers = vi.fn(() => 'preserved')
@@ -127,14 +127,13 @@ test('root route hydration preserves component state across its Suspense boundar
   })
   await router.load()
 
-  // Model the server render and the client router produced by hydrate(). The
-  // outer root boundary is intentionally absent from both trees, while the
-  // route's own pending boundary is present in both.
+  // Model the server render and the client router produced by hydrate(). A root
+  // without a separate shell stays unwrapped on both sides of hydration.
   router.ssr = { manifest: { routes: {} } }
   router.isServer = true
   const html = renderToString(<RouterProvider router={router} />)
   router.isServer = false
-  expect(html).toContain('<!--$-->')
+  expect(html).not.toContain('<!--$-->')
   expect(html).toContain('preserved')
 
   const container = document.createElement('div')
@@ -153,19 +152,48 @@ test('root route hydration preserves component state across its Suspense boundar
   })
 
   expect(container).toHaveTextContent('preserved')
-  // One initializer belongs to the server render and one to client
-  // hydration. The stable boundary must preserve that hydrated client
-  // instance instead of creating a third one.
+  // One initializer belongs to the server render and one to client hydration.
   expect(initializers).toHaveBeenCalledTimes(2)
   expect(mounts).toHaveBeenCalledTimes(1)
   expect(unmounts).not.toHaveBeenCalled()
   expect(consoleError).not.toHaveBeenCalled()
 })
 
-test('server rendering uses the root pending boundary for route component suspension', async () => {
+test('an unresolved functional ssr option does not enable a root pending boundary', async () => {
+  const rootRoute = createRootRoute({
+    ssr: () => true,
+    pendingComponent: () => <div>Root pending</div>,
+    component: () => <div>Root content</div>,
+  })
+  const router = createRouter({
+    routeTree: rootRoute,
+    history: createMemoryHistory({ initialEntries: ['/'] }),
+  })
+  await router.load()
+
+  const match = router.stores.matches.get()[0]!
+  expect(typeof match.ssr).toBe('function')
+
+  // Client match construction can expose the unresolved route option before
+  // hydration replaces it with its transported value.
+  router.ssr = { manifest: { routes: {} } }
+  router.isServer = true
+  const html = renderToString(<RouterProvider router={router} />)
+
+  expect(html).not.toContain('<!--$-->')
+  expect(html).toContain('Root content')
+})
+
+test('server rendering uses the root pending boundary inside its document shell', async () => {
   const gate = createControlledPromise<void>()
   const rootRoute = createRootRoute({
     pendingComponent: () => <div>Server root pending</div>,
+    shellComponent: ({ children }) => (
+      <html>
+        <head />
+        <body>{children}</body>
+      </html>
+    ),
     component: () => {
       throw gate
     },
@@ -179,8 +207,7 @@ test('server rendering uses the root pending boundary for route component suspen
 
   const html = renderToString(<RouterProvider router={router} />)
 
-  // renderToString cannot wait for Suspense, but the root route's stable
-  // boundary contains the suspension and emits its fallback. Streaming SSR
-  // can wait for the same boundary instead.
+  // renderToString cannot wait for Suspense, but the boundary inside the root
+  // shell contains the suspension and emits its fallback.
   expect(html).toContain('Server root pending')
 })
diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml
index 99fb327308..ca1175e9f2 100644
--- a/pnpm-lock.yaml
+++ b/pnpm-lock.yaml
@@ -3083,6 +3083,52 @@ importers:
         specifier: ^5.7.2
         version: 5.9.3
 
+  e2e/react-start/root-document-hydration:
+    dependencies:
+      '@tanstack/react-router':
+        specifier: workspace:*
+        version: link:../../../packages/react-router
+      '@tanstack/react-start':
+        specifier: workspace:*
+        version: link:../../../packages/react-start
+      react:
+        specifier: ^19.2.3
+        version: 19.2.3
+      react-dom:
+        specifier: ^19.2.3
+        version: 19.2.3(react@19.2.3)
+    devDependencies:
+      '@playwright/test':
+        specifier: ^1.61.0
+        version: 1.61.1
+      '@tanstack/router-e2e-utils':
+        specifier: workspace:*
+        version: link:../../e2e-utils
+      '@types/node':
+        specifier: 25.0.9
+        version: 25.0.9
+      '@types/react':
+        specifier: ^19.2.8
+        version: 19.2.9
+      '@types/react-dom':
+        specifier: ^19.2.3
+        version: 19.2.3(@types/react@19.2.9)
+      '@typescript/native':
+        specifier: npm:typescript@^7.0.2
+        version: typescript@7.0.2
+      '@vitejs/plugin-react':
+        specifier: ^6.0.1
+        version: 6.0.1(vite@8.0.14(@types/node@25.0.9)(esbuild@0.27.4)(jiti@2.7.0)(sass@1.97.2)(terser@5.37.0)(tsx@4.20.3)(yaml@2.9.0))
+      srvx:
+        specifier: ^0.11.9
+        version: 0.11.12
+      typescript:
+        specifier: npm:@typescript/typescript6@^6.0.2
+        version: '@typescript/typescript6@6.0.2'
+      vite:
+        specifier: ^8.0.14
+        version: 8.0.14(@types/node@25.0.9)(esbuild@0.27.4)(jiti@2.7.0)(sass@1.97.2)(terser@5.37.0)(tsx@4.20.3)(yaml@2.9.0)
+
   e2e/react-start/scroll-restoration:
     dependencies:
       '@tanstack/react-router':