diff --git a/packages/nuqs/src/adapters/tanstack-router.ts b/packages/nuqs/src/adapters/tanstack-router.ts
index 3ec90639b..b7879ce69 100644
--- a/packages/nuqs/src/adapters/tanstack-router.ts
+++ b/packages/nuqs/src/adapters/tanstack-router.ts
@@ -1,10 +1,42 @@
-import { useLocation, useMatches, useNavigate } from '@tanstack/react-router'
-import { startTransition, useCallback, useMemo } from 'react'
+import {
+  stringifySearchWith,
+  parseSearchWith,
+  useLocation,
+  useMatches,
+  useNavigate,
+  type AnySchema
+} from '@tanstack/react-router'
+import {
+  createContext,
+  createElement,
+  startTransition,
+  useCallback,
+  useContext,
+  useMemo,
+  type ReactElement,
+  type ReactNode
+} from 'react'
 import { renderQueryString } from '../lib/url-encoding'
-import { createAdapterProvider, type AdapterProvider } from './lib/context'
+import { createAdapterProvider, type AdapterProps } from './lib/context'
 import type { AdapterInterface, UpdateUrlFunction } from './lib/defs'
 
+// Use TanStack Router's default JSON-based search param serialization
+// The default behavior is compatible with nuqs' expected behavior
+const defaultStringifySearch = stringifySearchWith(JSON.stringify)
+const defaultParseSearch = parseSearchWith(JSON.parse)
+
+type TanstackRouterAdapterContextType = {
+  stringifySearchWith?: (search: Record<string, any>) => string
+}
+
+const NuqsTanstackRouterAdapterContext =
+  createContext<TanstackRouterAdapterContextType>({
+    stringifySearchWith: undefined
+  })
+
 function useNuqsTanstackRouterAdapter(watchKeys: string[]): AdapterInterface {
+  const { stringifySearchWith } = useContext(NuqsTanstackRouterAdapterContext)
+
   const search = useLocation({
     select: state =>
       Object.fromEntries(
@@ -18,32 +50,33 @@ function useNuqsTanstackRouterAdapter(watchKeys: string[]): AdapterInterface {
         ? (matches[matches.length - 1]?.fullPath as string)
         : undefined
   })
-  const searchParams = useMemo(
-    () =>
-      // search is a Record<string, string | number | object | Array<string | number>>,
-      // so we need to flatten it into a list of key/value pairs,
-      // replicating keys that have multiple values before passing it
-      // to URLSearchParams, otherwise { foo: ['bar', 'baz'] }
-      // ends up as { foo → 'bar,baz' } instead of { foo → 'bar', foo → 'baz' }
-      new URLSearchParams(
-        Object.entries(search).flatMap(([key, value]) => {
-          if (Array.isArray(value)) {
-            return value.map(v => [key, v])
-          } else if (typeof value === 'object' && value !== null) {
-            // TSR JSON.parses objects in the search params,
-            // but parseAsJson expects a JSON string,
-            // so we need to re-stringify it first.
-            return [[key, JSON.stringify(value)]]
-          } else {
-            return [[key, value]]
-          }
-        })
-      ),
-    [search, watchKeys.join(',')]
-  )
+  const searchParams = useMemo(() => {
+    // Regardless of whether the user specified a custom parseSearchWith,
+    // the search object here is already the result after parsing.
+    // We use the default defaultStringifySearch to convert the search
+    // to search params that nuqs can handle correctly.
+    //
+    // Use TSR's default stringify to convert search object → URLSearchParams.
+    // This avoids issues where arrays/objects were previously flattened
+    // into invalid values like "[object Object]".
+    return new URLSearchParams(defaultStringifySearch(search))
+  }, [search, watchKeys.join(',')])
 
   const updateUrl: UpdateUrlFunction = useCallback(
     (search, options) => {
+      let processedSearch: URLSearchParams
+      if (stringifySearchWith) {
+        // When updating, the search (URLSearchParams) here is in nuqs-generated format.
+        // We first use defaultParseSearch to parse it into a search object,
+        // then use the custom stringifySearchWith to convert it to a new URLSearchParams.
+        const searchObject = defaultParseSearch(search.toString())
+        const customQueryString = stringifySearchWith(searchObject)
+        processedSearch = new URLSearchParams(customQueryString)
+      } else {
+        // Use default behavior which is compatible with nuqs' expected behavior
+        processedSearch = search
+      }
+
       // Wrapping in a startTransition seems to be necessary
       // to support scroll restoration
       startTransition(() => {
@@ -59,7 +92,7 @@ function useNuqsTanstackRouterAdapter(watchKeys: string[]): AdapterInterface {
           // When we clear the search, passing an empty string causes
           // a type error and possible basepath issues, so we switch it to '.' instead.
           // See https://github.com/47ng/nuqs/pull/953#issuecomment-3003583471
-          to: renderQueryString(search) || '.',
+          to: renderQueryString(processedSearch) || '.',
           // `from` will be handled by tanstack router match resolver, code snippet:
           // https://github.com/TanStack/router/blob/5d940e2d8bdb12e213eede0abe8012855433ec4b/packages/react-router/src/link.tsx#L108-L112
           ...(from ? { from } : {}),
@@ -69,7 +102,7 @@ function useNuqsTanstackRouterAdapter(watchKeys: string[]): AdapterInterface {
         })
       })
     },
-    [navigate, from]
+    [navigate, from, stringifySearchWith]
   )
 
   return {
@@ -79,6 +112,21 @@ function useNuqsTanstackRouterAdapter(watchKeys: string[]): AdapterInterface {
   }
 }
 
-export const NuqsAdapter: AdapterProvider = createAdapterProvider(
+const NuqsTanstackRouterAdapter = createAdapterProvider(
   useNuqsTanstackRouterAdapter
 )
+
+export function NuqsAdapter({
+  children,
+  stringifySearchWith,
+  ...adapterProps
+}: AdapterProps & {
+  children: ReactNode
+  stringifySearchWith?: (search: Record<string, any>) => string
+}): ReactElement {
+  return createElement(
+    NuqsTanstackRouterAdapterContext.Provider,
+    { value: { stringifySearchWith } },
+    createElement(NuqsTanstackRouterAdapter, { ...adapterProps, children })
+  )
+}