diff --git a/.changeset/warm-notes-stay.md b/.changeset/warm-notes-stay.md
new file mode 100644
index 00000000..31c52cd1
--- /dev/null
+++ b/.changeset/warm-notes-stay.md
@@ -0,0 +1,5 @@
+---
+'@tanstack/typedoc-config': patch
+---
+
+fix(typedoc-config): add 'DO NOT EDIT' comment to generated pages via 'markdownHooks'
diff --git a/packages/typedoc-config/src/typedoc-custom-settings.ts b/packages/typedoc-config/src/typedoc-custom-settings.ts
index 89b2dcf3..c5f536e0 100644
--- a/packages/typedoc-config/src/typedoc-custom-settings.ts
+++ b/packages/typedoc-config/src/typedoc-custom-settings.ts
@@ -8,7 +8,11 @@ export function load(app: MarkdownApplication): void {
       id: page.model.name,
       title: page.model.name,
     }
-    page.contents =
-      '<!-- DO NOT EDIT: this page is autogenerated from the type comments -->\n\n'
   })
+
+  // Add a warning comment to the top of each page, including the index page
+  const doNotEdit = () =>
+    '<!-- DO NOT EDIT: this page is autogenerated from the type comments -->'
+  app.renderer.markdownHooks.on('page.begin', doNotEdit)
+  app.renderer.markdownHooks.on('index.page.begin', doNotEdit)
 }