diff --git a/src/project/types/website/website-llms.ts b/src/project/types/website/website-llms.ts
index 78e7fcaed6..5b8431f31e 100644
--- a/src/project/types/website/website-llms.ts
+++ b/src/project/types/website/website-llms.ts
@@ -147,10 +147,12 @@ function extractMainContent(doc: Document): string {
   }
 
   // Get the main content area
+  // Note: use querySelector("body") instead of clone.body because
+  // deno-dom's cloneNode() doesn't preserve the .body convenience getter
   const main = clone.querySelector("main") ||
     clone.querySelector("#quarto-document-content") ||
     clone.querySelector("article") ||
-    clone.body;
+    clone.querySelector("body");
 
   if (!main) {
     return "";
diff --git a/tests/docs/smoke-all/website/llms-txt/_quarto.yml b/tests/docs/smoke-all/website/llms-txt/_quarto.yml
index 16837fcbd9..56fb6e0117 100644
--- a/tests/docs/smoke-all/website/llms-txt/_quarto.yml
+++ b/tests/docs/smoke-all/website/llms-txt/_quarto.yml
@@ -11,6 +11,7 @@ website:
       - href: index.qmd
         text: Home
       - about.qmd
+      - custom-layout.qmd
   sidebar:
     contents:
       - section: Info
diff --git a/tests/docs/smoke-all/website/llms-txt/custom-layout.qmd b/tests/docs/smoke-all/website/llms-txt/custom-layout.qmd
new file mode 100644
index 0000000000..09bc15e2cc
--- /dev/null
+++ b/tests/docs/smoke-all/website/llms-txt/custom-layout.qmd
@@ -0,0 +1,50 @@
+---
+pagetitle: "Custom Layout Page"
+page-layout: custom
+section-divs: false
+toc: false
+_quarto:
+  tests:
+    html:
+      ensureLlmsMdExists: true
+      ensureLlmsMdRegexMatches:
+        - ["Welcome to the Custom Page", "Feature One", "Feature Two", "Learn more"]
+        - []
+---
+
+::: {.hero-banner}
+::: {.content-block}
+
+# Welcome to the Custom Page
+
+### A page using custom layout
+
+- This tests that llms-txt works with page-layout: custom.
+- Custom layout pages lack a `<main>` element in the rendered HTML.
+
+:::
+:::
+
+::: {.content-block}
+::: {.features}
+
+::: {.feature}
+### Feature One
+Description of the first feature.
+
+::: {.learn-more}
+[Learn more »](about.qmd)
+:::
+:::
+
+::: {.feature}
+### Feature Two
+Description of the second feature.
+
+::: {.learn-more}
+[Learn more »](about.qmd)
+:::
+:::
+
+:::
+:::