diff --git a/frontend/src/features/layout/LayoutGrid.cellControlsLayering.test.tsx b/frontend/src/features/layout/LayoutGrid.cellControlsLayering.test.tsx
index e862a294..7c2b8cb6 100644
--- a/frontend/src/features/layout/LayoutGrid.cellControlsLayering.test.tsx
+++ b/frontend/src/features/layout/LayoutGrid.cellControlsLayering.test.tsx
@@ -206,27 +206,40 @@ describe("LayoutGrid — ticket #48 cell control layering", () => {
     expect(controls.style.overflow).toBe("hidden");
   });
 
-  it("keeps cell controls above the custom CLI view stacking context", async () => {
+  it("does not render persistent cell chrome over the custom CLI surface (#249)", async () => {
     const setup = await makeSplitAgentGrid();
     window.localStorage.setItem(`idea.agent-cell-mode.p1.${setup.bId}`, "custom");
+    setup.workState._setProjectWorkState("p1", {
+      agents: [
+        {
+          agentId: setup.agentId,
+          name: "Worker",
+          profileId: "mock-claude",
+          busy: { state: "busy", sinceMs: 1 },
+        },
+      ],
+    });
 
     renderGrid(setup.gateways);
 
     await screen.findByTestId("custom-agent-chat-view");
     window.localStorage.removeItem(`idea.agent-cell-mode.p1.${setup.bId}`);
-    const leafBody = screen.getAllByTestId("layout-leaf-body").find((element) =>
-      element.closest(`[data-node-id="${setup.bId}"]`),
-    ) as HTMLElement;
     const customToolbar = screen.getByRole("toolbar", {
       name: "custom agent chat actions",
     });
-    const { controls } = controlsFor(setup.bId);
 
-    expect(leafBody).toBeTruthy();
-    expect(leafBody.style.position).toBe("relative");
-    expect(leafBody.style.zIndex).toBe("0");
     expect(customToolbar.className).toContain("z-20");
-    expect(controls.style.zIndex).toBe("5");
+    expect(screen.queryByLabelText(`agent selector ${setup.bId}`)).toBeNull();
+    expect(screen.queryByRole("group", {
+      name: `mode CLI agent ${setup.bId}`,
+    })).toBeNull();
+    expect(screen.queryByLabelText(`split ${setup.bId} columns`)).toBeNull();
+    expect(screen.queryByLabelText(`split ${setup.bId} rows`)).toBeNull();
+    expect(screen.queryByLabelText(`close ${setup.bId}`)).toBeNull();
+    expect(screen.queryByRole("button", {
+      name: `cancel current turn ${setup.bId}`,
+    })).toBeNull();
+    expect(screen.queryByText("Busy")).toBeNull();
   });
 
   it("keeps busy Cancel above persistent cell controls and removes History (#151, #160)", async () => {
diff --git a/frontend/src/features/layout/LayoutGrid.chat.test.tsx b/frontend/src/features/layout/LayoutGrid.chat.test.tsx
index 5091bab6..f082b2e1 100644
--- a/frontend/src/features/layout/LayoutGrid.chat.test.tsx
+++ b/frontend/src/features/layout/LayoutGrid.chat.test.tsx
@@ -219,7 +219,11 @@ describe("LayoutGrid custom agent CLI (#147)", () => {
 
     expect(await screen.findByTestId("custom-agent-chat-view")).toBeTruthy();
     expect(screen.queryByTestId("target-announcements-overlay")).toBeNull();
-    expect(screen.getByText("Busy · Main")).toBeTruthy();
+    expect(screen.queryByText("Busy · Main")).toBeNull();
+    expect(screen.queryByLabelText(`agent selector ${leaf.id}`)).toBeNull();
+    expect(screen.queryByRole("button", {
+      name: `cancel current turn ${leaf.id}`,
+    })).toBeNull();
     await waitFor(() =>
       expect(screen.getByLabelText(/message CLI custom/)).toHaveProperty(
         "disabled",
diff --git a/frontend/src/features/layout/LayoutGrid.tsx b/frontend/src/features/layout/LayoutGrid.tsx
index c99802f3..aa0754f0 100644
--- a/frontend/src/features/layout/LayoutGrid.tsx
+++ b/frontend/src/features/layout/LayoutGrid.tsx
@@ -655,6 +655,13 @@ function LeafView({
     customCliAvailable && pinnedAgent ? pinnedAgent : trustedCustomCli?.agent;
   const customCliProfile =
     customCliAvailable && pinnedProfile ? pinnedProfile : trustedCustomCli?.profile;
+  const customCliActive = Boolean(
+    agentId &&
+      cellMode === "custom" &&
+      effectiveCustomCliAvailable &&
+      customCliAgent &&
+      customCliProfile,
+  );
   useEffect(() => {
     if (cellMode !== "custom") {
       setTrustedCustomCli(null);
@@ -767,6 +774,7 @@ function LeafView({
       task.status === "completed" || task.status === "failed" || task.status === "cancelled",
     ) ?? [];
   const busyByWorkState = agentWork?.busy.state === "busy" || Boolean(activeTicket);
+  const suppressCellChrome = customCliActive && busyByWorkState;
   const delegatedTicket = activeTicket?.source.kind === "agent" ? activeTicket : undefined;
   const busyActive = announcementBusyActive || busyByWorkState;
   const targetAnnouncementsFallback = delegatedTicket?.requesterLabel
@@ -1130,25 +1138,27 @@ function LeafView({
         overflow: "hidden",
       }}
     >
-      <div
-        style={{
-          position: "absolute",
-          top: 2,
-          left: 4,
-          // Clear the xterm viewport scrollbar (rendered flush against the right
-          // edge, ~15px wide). Without this offset the right-most control — the
-          // close button — sits *behind* the scrollbar and is hard to click.
-          right: 16,
-          // Above every banner/veil so a cell in an error state stays manageable
-          // (ticket #48).
-          zIndex: CELL_Z.controls,
-          display: "flex",
-          gap: 2,
-          alignItems: "center",
-          justifyContent: "flex-end",
-          overflow: "hidden",
-        }}
-      >
+      {!suppressCellChrome && (
+        <div
+          style={{
+            position: "absolute",
+            top: 2,
+            left: 4,
+            // Clear the xterm viewport scrollbar (rendered flush against the right
+            // edge, ~15px wide). Without this offset the right-most control — the
+            // close button — sits *behind* the scrollbar and is hard to click.
+            right: 16,
+            // Above every banner/veil so a cell in an error state stays manageable
+            // (ticket #48). Hidden while a custom CLI turn is busy: that surface
+            // owns its own header, and cell chrome must not overlap the chat viewport.
+            zIndex: CELL_Z.controls,
+            display: "flex",
+            gap: 2,
+            alignItems: "center",
+            justifyContent: "flex-end",
+            overflow: "hidden",
+          }}
+        >
         {/* Agent selector */}
         <select
           aria-label={`agent selector ${id}`}
@@ -1320,8 +1330,9 @@ function LeafView({
             ✕
           </button>
         )}
-      </div>
-      {agentId && busyByWorkState && (
+        </div>
+      )}
+      {agentId && busyByWorkState && !suppressCellChrome && (
         <button
           type="button"
           aria-label={`cancel current turn ${id}`}
@@ -1347,7 +1358,7 @@ function LeafView({
           Cancel
         </button>
       )}
-      {agentId && (busyByWorkState || inboxDepth > 0 || completedBackgroundTasks.length > 0) && (
+      {agentId && !suppressCellChrome && (busyByWorkState || inboxDepth > 0 || completedBackgroundTasks.length > 0) && (
         <div
           role="status"
           aria-live="polite"