diff --git a/src/features/tmux-subagent/action-executor.ts b/src/features/tmux-subagent/action-executor.ts
index 0ebbd4378..afdddfbf8 100644
--- a/src/features/tmux-subagent/action-executor.ts
+++ b/src/features/tmux-subagent/action-executor.ts
@@ -61,13 +61,30 @@ async function enforceLayoutAndMainPane(ctx: ExecuteContext): Promise<void> {
   await enforceMainPane(latestState, ctx.config)
 }
 
+/**
+ * Returns true when the pane lives in the source window's tracked layout.
+ *
+ * The wrapper enforces the user's main-vertical layout against the source pane
+ * after destructive actions. That is correct when the affected pane was part of
+ * the source window (its removal changes the user's split arrangement) but
+ * actively harmful when the pane lived in a separate window — closing an
+ * isolated container in another window should not scramble the user's main
+ * window layout. Callers route both cases through the same close action, so we
+ * detect the relationship from `windowState`.
+ */
+function isPaneInSourceWindow(paneId: string, windowState: WindowState): boolean {
+  if (windowState.mainPane?.paneId === paneId) return true
+  return windowState.agentPanes.some((pane) => pane.paneId === paneId)
+}
+
 export async function executeAction(
   action: PaneAction,
   ctx: ExecuteContext
 ): Promise<ActionResult> {
   if (action.type === "close") {
+    const closingPaneInSourceWindow = isPaneInSourceWindow(action.paneId, ctx.windowState)
     const success = await closeTmuxPane(action.paneId)
-    if (success) {
+    if (success && closingPaneInSourceWindow) {
       await enforceLayoutAndMainPane(ctx)
     }
     return { success }