diff --git a/src/tui/mention-popup.test.ts b/src/tui/mention-popup.test.ts
index b903e9dcc..ee7ba5ae7 100644
--- a/src/tui/mention-popup.test.ts
+++ b/src/tui/mention-popup.test.ts
@@ -2,13 +2,16 @@
  * Integration: the `@` path popup narrows as you type, the same contract the
  * `/` command popup already honours.
  */
+import { EventEmitter } from "node:events"
 import { describe, expect, test } from "bun:test"
 
 import type { KeyEvent } from "@opentui/core"
 
+import { wireGates } from "./gate-wire"
 import { withTestRenderer } from "./harness"
 import {
   acceptOverlaySelection,
+  closeMentionPopup,
   createAppShell,
   handleMentionPopupKey,
   isMentionPopupOpen,
@@ -224,4 +227,64 @@ describe("@ popup narrows as you type", () => {
       ])
     })
   })
+
+  // CL-6698: a queued permission/operator gate must not open onto the host
+  // in the middle of a mention filter session. The old close-then-reopen
+  // refresh released the host between the two calls, and a gate queued
+  // behind the popup drained into that gap — leaving the gate's overlay on
+  // screen while `mentionPopups` still (wrongly) claimed ownership, so
+  // further keystrokes went nowhere.
+  test("a queued gate stays queued across a mention filter refresh", async () => {
+    await withShell(async (shell) => {
+      const emitter = new EventEmitter()
+      const dispose = wireGates(emitter, shell)
+      try {
+        await openAt(shell, "@")
+        expect(isMentionPopupOpen(shell)).toBe(true)
+
+        let resolved: unknown
+        emitter.emit("permission.gate", {
+          request: {
+            tool: "run_shell",
+            action: "Run shell command",
+            subject: "bun test",
+            scopes: [],
+          },
+          resolve: (outcome: unknown) => {
+            resolved = outcome
+          },
+        })
+
+        // Queued, not opened — the mention popup still owns the host.
+        expect(shell.overlayKind).toBe("mentions")
+        expect(resolved).toBeUndefined()
+
+        // Refreshing the filter must not release the host to the queued gate.
+        expect(await type(shell, printable("s"))).toBe(true)
+        expect(shell.prompt.value).toBe("@s")
+        expect(shell.overlayKind).toBe("mentions")
+        expect(isMentionPopupOpen(shell)).toBe(true)
+        expect(shell.overlayItems).toEqual([
+          "session-notes.md",
+          "src/",
+          "AGENTS.md",
+        ])
+        expect(resolved).toBeUndefined()
+
+        // Mention filtering keeps working after the refresh.
+        await type(shell, printable("e"))
+        expect(shell.prompt.value).toBe("@se")
+        expect(shell.overlayItems).toEqual(["session-notes.md"])
+        expect(isMentionPopupOpen(shell)).toBe(true)
+        expect(resolved).toBeUndefined()
+
+        // A true dismiss still drains the queue as before.
+        closeMentionPopup(shell)
+        expect(shell.overlayKind).toBe("permissions")
+        expect(resolved).toBeUndefined()
+      } finally {
+        dispose()
+      }
+    })
+  })
 })
diff --git a/src/tui/shell.ts b/src/tui/shell.ts
index 89c6360ad..cbe8e1451 100644
--- a/src/tui/shell.ts
+++ b/src/tui/shell.ts
@@ -5052,16 +5052,33 @@ export async function openAtMentionSuggestions(shell: AppShell): Promise<boolean
     return false
   }
 
+  // The onAccept closure reads through this ref rather than closing over
+  // `suggestions`/`at`/`cursor` directly, so a same-session refresh can
+  // update what accept splices without re-binding the callback.
+  mentionAcceptState.set(shell, { suggestions, atStart: at.atStart, cursor })
+
+  // Every keystroke lands here while the popup is already open. Closing and
+  // reopening the overlay released the host between the two calls — long
+  // enough for a queued permission/operator gate to open on it — and left the
+  // gate's overlay on screen while `mentionPopups` still claimed ownership.
+  // Refreshing the open list in place never releases the host, so a queued
+  // gate has nothing to drain into.
+  if (isMentionPopupOpen(shell)) {
+    setOverlayItems(shell, [...suggestions])
+    return true
+  }
+
   closeMentionPopup(shell)
   openMentionsOverlay(shell, {
     items: [...suggestions],
     onAccept: (selection) => {
-      const completion = suggestions[selection.index]
-      if (completion === undefined) return
+      const state = mentionAcceptState.get(shell)
+      const completion = state?.suggestions[selection.index]
+      if (completion === undefined || state === undefined) return
       const spliced = spliceMentionCompletion(
         shell.prompt.value,
-        at.atStart,
-        cursor,
+        state.atStart,
+        state.cursor,
         completion,
       )
       shell.prompt.value = spliced.value
@@ -5076,6 +5093,12 @@ export async function openAtMentionSuggestions(shell: AppShell): Promise<boolean
 
 const mentionPopups = new WeakSet<AppShell>()
 const mentionGenerations = new WeakMap<AppShell, number>()
+type MentionAcceptState = {
+  readonly suggestions: readonly string[]
+  readonly atStart: number
+  readonly cursor: number
+}
+const mentionAcceptState = new WeakMap<AppShell, MentionAcceptState>()
 
 /** True while the `@` path popup owns typed characters. */
 export function isMentionPopupOpen(shell: AppShell): boolean {