diff --git a/src/app.ts b/src/app.ts
index adfad5c77..c43135e0f 100644
--- a/src/app.ts
+++ b/src/app.ts
@@ -1828,10 +1828,11 @@ export class App extends ProtocolWithEvents<
   }
 
   /**
-   * Set up automatic size change notifications using ResizeObserver.
+   * Set up automatic size change notifications using ResizeObserver and MutationObserver.
    *
-   * Observes both `document.documentElement` and `document.body` for size changes
-   * and automatically sends `ui/notifications/size-changed` notifications to the host.
+   * Observes both `document.documentElement` and `document.body` for size changes,
+   * and the document for mutations that can affect out-of-flow content such as portals.
+   * Automatically sends `ui/notifications/size-changed` notifications to the host.
    * The notifications are debounced using requestAnimationFrame to avoid duplicates.
    *
    * Note: This method is automatically called by `connect()` if the `autoResize`
@@ -1858,6 +1859,7 @@ export class App extends ProtocolWithEvents<
    */
   setupSizeChangedNotifications() {
     let scheduled = false;
+    let animationFrameId: number | undefined;
     let lastWidth = 0;
     let lastHeight = 0;
 
@@ -1866,7 +1868,7 @@ export class App extends ProtocolWithEvents<
         return;
       }
       scheduled = true;
-      requestAnimationFrame(() => {
+      animationFrameId = requestAnimationFrame(() => {
         scheduled = false;
         const html = document.documentElement;
 
@@ -1882,8 +1884,46 @@ export class App extends ProtocolWithEvents<
         // destroying their scroll positions.
         const originalHeight = html.style.height;
         html.style.height = "max-content";
-        const height = Math.ceil(html.getBoundingClientRect().height);
+        const htmlRect = html.getBoundingClientRect();
+        let height = htmlRect.height;
+
+        // Out-of-flow descendants (for example, menus rendered in a portal)
+        // do not contribute to the html element's intrinsic height.
+        const clippingBottoms = new WeakMap<Element, number>();
+        const measureElement = (element: Element) => {
+          const rect = element.getBoundingClientRect();
+          const parentElement = element.parentElement;
+          const inheritedClippingBottom =
+            (parentElement && clippingBottoms.get(parentElement)) ?? Infinity;
+          height = Math.max(
+            height,
+            Math.min(rect.bottom, inheritedClippingBottom) - htmlRect.top,
+          );
+
+          if (element.childElementCount > 0) {
+            const overflowY = getComputedStyle(element).overflowY;
+            clippingBottoms.set(
+              element,
+              overflowY === "visible"
+                ? inheritedClippingBottom
+                : Math.min(rect.bottom, inheritedClippingBottom),
+            );
+          }
+        };
+        measureElement(document.body);
+        const treeWalker = document.createTreeWalker(
+          document.body,
+          NodeFilter.SHOW_ELEMENT,
+        );
+        let element = treeWalker.nextNode() as Element | null;
+        while (element) {
+          measureElement(element);
+          element = treeWalker.nextNode() as Element | null;
+        }
+
+        height = Math.ceil(height);
         html.style.height = originalHeight;
+        mutationObserver.takeRecords();
 
         const width = Math.ceil(window.innerWidth);
 
@@ -1903,7 +1943,21 @@ export class App extends ProtocolWithEvents<
     resizeObserver.observe(document.documentElement);
     resizeObserver.observe(document.body);
 
-    return () => resizeObserver.disconnect();
+    const mutationObserver = new MutationObserver(sendBodySizeChanged);
+    mutationObserver.observe(document.documentElement, {
+      attributes: true,
+      childList: true,
+      characterData: true,
+      subtree: true,
+    });
+
+    return () => {
+      resizeObserver.disconnect();
+      mutationObserver.disconnect();
+      if (animationFrameId !== undefined) {
+        cancelAnimationFrame(animationFrameId);
+      }
+    };
   }
 
   /**
diff --git a/tests/e2e/auto-resize.spec.ts b/tests/e2e/auto-resize.spec.ts
new file mode 100644
index 000000000..1d4f52c6b
--- /dev/null
+++ b/tests/e2e/auto-resize.spec.ts
@@ -0,0 +1,72 @@
+import { test, expect } from "@playwright/test";
+import { resolve } from "node:path";
+
+test("auto-resize tracks out-of-flow portal content", async ({ page }) => {
+  await page.route("**/app-with-deps.js", (route) =>
+    route.fulfill({
+      contentType: "text/javascript",
+      path: resolve("dist/src/app-with-deps.js"),
+    }),
+  );
+  await page.goto("/");
+
+  const sizes = await page.evaluate(async () => {
+    document.open();
+    document.write(`<!doctype html>
+      <style>
+        html, body { margin: 0; }
+        #content { height: 100px; }
+        #portal { position: absolute; top: 300px; height: 100px; }
+        .scroll { height: 100px; overflow: auto; }
+        .scroll-content { height: 1000px; }
+      </style>
+      <div id="content"></div>`);
+    document.close();
+
+    const { App } = await import("/app-with-deps.js");
+    const app = new App(
+      { name: "auto-resize-test", version: "1.0.0" },
+      {},
+      { autoResize: false },
+    );
+    const reportedSizes: Array<{ width?: number; height?: number }> = [];
+    app.sendSizeChanged = async (size) => {
+      reportedSizes.push(size);
+    };
+
+    const waitForMeasurement = async () => {
+      await new Promise((resolve) => requestAnimationFrame(resolve));
+      await new Promise((resolve) => requestAnimationFrame(resolve));
+    };
+
+    const cleanup = app.setupSizeChangedNotifications();
+    await waitForMeasurement();
+
+    const portal = document.createElement("div");
+    portal.id = "portal";
+    document.body.append(portal);
+    await waitForMeasurement();
+
+    portal.style.top = "500px";
+    await waitForMeasurement();
+
+    portal.remove();
+    await waitForMeasurement();
+
+    document.body.innerHTML =
+      '<div class="scroll"><div class="scroll-content"></div></div>';
+    await waitForMeasurement();
+
+    document.body.style.cssText = "height: 120px; overflow: auto";
+    document.body.innerHTML = '<div class="scroll-content"></div>';
+    await waitForMeasurement();
+
+    cleanup();
+    document.body.append(portal);
+    await waitForMeasurement();
+
+    return reportedSizes;
+  });
+
+  expect(sizes.map(({ height }) => height)).toEqual([100, 400, 600, 100, 120]);
+});