diff --git a/src/generators/jsx-ast/utils/__tests__/transformer.test.mjs b/src/generators/jsx-ast/utils/__tests__/transformer.test.mjs
new file mode 100644
index 00000000..4b7df072
--- /dev/null
+++ b/src/generators/jsx-ast/utils/__tests__/transformer.test.mjs
@@ -0,0 +1,42 @@
+import assert from 'node:assert/strict';
+import { describe, it } from 'node:test';
+
+import transformer from '../transformer.mjs';
+
+describe('jsx-ast transformer', () => {
+  it('moves generated footnotes into the Layout children', () => {
+    const layout = {
+      type: 'mdxJsxTextElement',
+      name: 'Layout',
+      children: [{ type: 'element', tagName: 'p', children: [] }],
+    };
+    const footnotes = {
+      type: 'element',
+      tagName: 'section',
+      properties: { dataFootnotes: '', className: ['footnotes'] },
+      children: [
+        {
+          type: 'element',
+          tagName: 'ol',
+          children: [
+            {
+              type: 'element',
+              tagName: 'li',
+              properties: { id: 'user-content-fn-a' },
+              children: [{ type: 'text', value: 'Footnote text' }],
+            },
+          ],
+        },
+      ],
+    };
+    const tree = {
+      type: 'root',
+      children: [layout, { type: 'text', value: '\n' }, footnotes],
+    };
+
+    transformer()(tree);
+
+    assert.equal(tree.children.includes(footnotes), false);
+    assert.equal(layout.children.at(-1), footnotes);
+  });
+});
diff --git a/src/generators/jsx-ast/utils/transformer.mjs b/src/generators/jsx-ast/utils/transformer.mjs
index b5c732ff..53dadee7 100644
--- a/src/generators/jsx-ast/utils/transformer.mjs
+++ b/src/generators/jsx-ast/utils/transformer.mjs
@@ -3,6 +3,23 @@ import { visit } from 'unist-util-visit';
 
 import { TAG_TRANSFORMS } from '../constants.mjs';
 
+/**
+ * Checks whether a HAST node is the generated GFM footnotes section.
+ * @param {import('hast').Element} node
+ */
+const isFootnotesSection = node =>
+  node?.type === 'element' &&
+  node.tagName === 'section' &&
+  (node.properties?.dataFootnotes !== undefined ||
+    node.properties?.className?.includes('footnotes'));
+
+/**
+ * Finds the generated page Layout node.
+ * @param {import('hast').Root} tree
+ */
+const findLayout = tree =>
+  tree.children.find(node => node.name === 'Layout' && node.children);
+
 /**
  * @template {import('unist').Node} T
  * @param {T} tree
@@ -43,14 +60,17 @@ const transformer = tree => {
     }
   });
 
-  // Are there footnotes?
-  if (tree.children.at(-1).tagName === 'section') {
-    const section = tree.children.pop();
-    // If so, move it into the proper location
-    // Root -> Article -> Main content
-    tree.children[2]?.children[1]?.children[0]?.children?.push(
-      ...section.children
-    );
+  const index = tree.children.findLastIndex(isFootnotesSection);
+
+  if (index !== -1) {
+    const [section] = tree.children.splice(index, 1);
+    const layout = findLayout(tree);
+
+    if (layout) {
+      layout.children.push(section);
+    } else {
+      tree.children.push(section);
+    }
   }
 };