diff --git a/packages/app/src/hooks/use-keyboard-shortcuts.ts b/packages/app/src/hooks/use-keyboard-shortcuts.ts
index d723b5be04..4354d364ff 100644
--- a/packages/app/src/hooks/use-keyboard-shortcuts.ts
+++ b/packages/app/src/hooks/use-keyboard-shortcuts.ts
@@ -40,7 +40,7 @@ import {
   navigateToLastWorkspace,
   useActiveWorkspaceSelection,
 } from "@/stores/navigation-active-workspace-store";
-import { dispatchTopWebOverlayKeyDown } from "@/lib/overlay-root";
+import { dispatchTopWebOverlayKeyDown, hasOpenDomPopover } from "@/lib/overlay-root";
 
 export function useKeyboardShortcuts({
   enabled,
@@ -321,6 +321,13 @@ export function useKeyboardShortcuts({
       return;
     }
 
+    // An open popover (a plugin's panel) is the top layer and closes on its
+    // own Escape listener, which runs after this one. Escape is not an app
+    // shortcut then: it must not also interrupt the running agent.
+    if (event.key === "Escape" && hasOpenDomPopover()) {
+      return;
+    }
+
     // During IME composition, Enter confirms the candidate selection and must
     // not route through global shortcuts like message send.
     if (isImeComposingKeyboardEvent(event)) {
diff --git a/packages/app/src/lib/overlay-root.browser.test.tsx b/packages/app/src/lib/overlay-root.browser.test.tsx
index a21403dd8d..8cf09fcf72 100644
--- a/packages/app/src/lib/overlay-root.browser.test.tsx
+++ b/packages/app/src/lib/overlay-root.browser.test.tsx
@@ -2,7 +2,7 @@ import React, { type RefCallback } from "react";
 import { flushSync } from "react-dom";
 import { createRoot, type Root } from "react-dom/client";
 import { afterEach, beforeEach, describe, expect, it } from "vitest";
-import { useWebOverlayRegistration } from "./overlay-root";
+import { hasOpenDomPopover, useWebOverlayRegistration } from "./overlay-root";
 
 function nextFrame(): Promise<void> {
   return new Promise((resolve) => requestAnimationFrame(() => resolve()));
@@ -68,3 +68,20 @@ describe("useWebOverlayRegistration in the browser", () => {
     expect(openerFocusCalls).toBe(1);
   });
 });
+
+describe("hasOpenDomPopover", () => {
+  afterEach(() => {
+    document.body.replaceChildren();
+  });
+
+  it("is true only while a popover is shown", () => {
+    const panel = document.createElement("div");
+    panel.setAttribute("popover", "manual");
+    document.body.append(panel);
+    expect(hasOpenDomPopover()).toBe(false);
+    panel.showPopover();
+    expect(hasOpenDomPopover()).toBe(true);
+    panel.hidePopover();
+    expect(hasOpenDomPopover()).toBe(false);
+  });
+});
diff --git a/packages/app/src/lib/overlay-root.ts b/packages/app/src/lib/overlay-root.ts
index 9ffd81725f..bb0ec6d168 100644
--- a/packages/app/src/lib/overlay-root.ts
+++ b/packages/app/src/lib/overlay-root.ts
@@ -112,6 +112,21 @@ export function hasActiveWebOverlay(): boolean {
   return getTopWebOverlay() !== undefined;
 }
 
+/**
+ * True while an element shown with the Popover API is open. Such a layer
+ * floats above the app like a registered overlay but lives outside the
+ * registry: plugins draw their panels this way, since they cannot register.
+ */
+export function hasOpenDomPopover(): boolean {
+  if (typeof document === "undefined") return false;
+  try {
+    return document.querySelector(":popover-open") !== null;
+  } catch {
+    // An engine without the Popover API rejects the selector, and has none open.
+    return false;
+  }
+}
+
 function getFocusableElements(scope: HTMLElement): HTMLElement[] {
   const selector = [
     "a[href]",