diff --git a/Sources/AppDelegate.swift b/Sources/AppDelegate.swift
index da05b90bbdc3..b3224bb044c0 100644
--- a/Sources/AppDelegate.swift
+++ b/Sources/AppDelegate.swift
@@ -10575,6 +10575,40 @@ final class AppDelegate: NSObject, NSApplicationDelegate, UNUserNotificationCent
         return true
     }
 
+    private func handleContextIndependentShortcut(event: NSEvent) -> Bool {
+        if matchConfiguredShortcut(event: event, action: .quit) {
+            return handleQuitShortcutWarning()
+        }
+
+        if matchConfiguredShortcut(event: event, action: .openSettings) {
+            openPreferencesWindow(debugSource: "shortcut.openSettings")
+            return true
+        }
+
+        if matchConfiguredShortcut(event: event, action: .reloadConfiguration) {
+            GhosttyApp.shared.reloadConfiguration(source: "shortcut.reloadConfiguration")
+            return true
+        }
+
+        if matchConfiguredShortcut(event: event, action: .newWindow) {
+            openNewMainWindow(preferredWindow: mainWindowForShortcutEvent(event))
+            return true
+        }
+
+        return false
+    }
+
+    private var contextIndependentShortcutActions: [KeyboardShortcutSettings.Action] {
+        // Keep main-window lifecycle commands, such as Close Window, on the synchronized
+        // path because their AppKit delegates depend on the active terminal context.
+        [
+            .quit,
+            .openSettings,
+            .reloadConfiguration,
+            .newWindow,
+        ]
+    }
+
     private func handleCustomShortcut(event: NSEvent) -> Bool {
         guard event.type == .keyDown else {
             clearConfiguredShortcutChordState()
@@ -10946,6 +10980,15 @@ final class AppDelegate: NSObject, NSApplicationDelegate, UNUserNotificationCent
             return true
         }
 
+        if handleContextIndependentShortcut(event: event) {
+            return true
+        }
+
+        if activeConfiguredShortcutChordPrefixForCurrentEvent == nil,
+           armConfiguredShortcutChordIfNeeded(event: event, actions: contextIndependentShortcutActions) {
+            return true
+        }
+
         let hasEventWindowContext = shortcutEventHasAddressableWindow(event)
         let didSynchronizeShortcutContext = synchronizeShortcutRoutingContext(event: event)
         if hasEventWindowContext && !didSynchronizeShortcutContext {
@@ -11036,18 +11079,6 @@ final class AppDelegate: NSObject, NSApplicationDelegate, UNUserNotificationCent
             return true
         }
 
-        if matchConfiguredShortcut(event: event, action: .quit) {
-            return handleQuitShortcutWarning()
-        }
-        if matchConfiguredShortcut(event: event, action: .openSettings) {
-            openPreferencesWindow(debugSource: "shortcut.openSettings")
-            return true
-        }
-        if matchConfiguredShortcut(event: event, action: .reloadConfiguration) {
-            GhosttyApp.shared.reloadConfiguration(source: "shortcut.reloadConfiguration")
-            return true
-        }
-
         if matchConfiguredShortcut(event: event, action: .toggleFullScreen) {
             guard let targetWindow = mainWindowForShortcutEvent(event) else {
                 return false
@@ -11078,15 +11109,6 @@ final class AppDelegate: NSObject, NSApplicationDelegate, UNUserNotificationCent
             return true
         }
 
-        // New Window: Cmd+Shift+N
-        // Handled here instead of relying on SwiftUI's CommandGroup menu item because
-        // after a browser panel has been shown, SwiftUI's menu dispatch can silently
-        // consume the key equivalent without firing the action closure.
-        if matchConfiguredShortcut(event: event, action: .newWindow) {
-            openNewMainWindow(preferredWindow: mainWindowForShortcutEvent(event))
-            return true
-        }
-
         // Open Folder: Cmd+O
         // Handled here to prevent AppKit's default NSDocumentController from opening
         // the Documents folder when SwiftUI menu dispatch fails due to focus bugs.
diff --git a/cmuxTests/AppDelegateShortcutRoutingTests.swift b/cmuxTests/AppDelegateShortcutRoutingTests.swift
index 52e2ab47db6b..fcfa41fac6bc 100644
--- a/cmuxTests/AppDelegateShortcutRoutingTests.swift
+++ b/cmuxTests/AppDelegateShortcutRoutingTests.swift
@@ -2791,6 +2791,61 @@ final class AppDelegateShortcutRoutingTests: XCTestCase {
         XCTAssertEqual(workspace.panels.count, panelCountBefore)
     }
 
+    func testCmdCommaOpensSettingsFromWindowWithoutTerminalShortcutContext() {
+        guard let appDelegate = AppDelegate.shared else {
+            XCTFail("Expected AppDelegate.shared")
+            return
+        }
+
+        let windowId = appDelegate.createMainWindow()
+        defer { closeWindow(withId: windowId) }
+
+        let auxiliaryWindow = NSWindow(
+            contentRect: NSRect(x: 0, y: 0, width: 360, height: 240),
+            styleMask: [.titled, .closable],
+            backing: .buffered,
+            defer: false
+        )
+        auxiliaryWindow.isReleasedWhenClosed = false
+        auxiliaryWindow.identifier = NSUserInterfaceItemIdentifier("cmux.shortcut-routing-test")
+        auxiliaryWindow.makeKeyAndOrderFront(nil)
+        RunLoop.main.run(until: Date(timeIntervalSinceNow: 0.05))
+        defer {
+            auxiliaryWindow.orderOut(nil)
+            auxiliaryWindow.close()
+            RunLoop.main.run(until: Date(timeIntervalSinceNow: 0.05))
+        }
+
+        var settingsOpenCount = 0
+#if DEBUG
+        SettingsWindowPresenter.resetForTests()
+        defer { SettingsWindowPresenter.resetForTests() }
+#endif
+        SettingsWindowPresenter.configure(openWindow: {
+            settingsOpenCount += 1
+        })
+
+        guard let event = makeKeyDownEvent(
+            key: ",",
+            modifiers: [.command],
+            keyCode: 43,
+            windowNumber: auxiliaryWindow.windowNumber
+        ) else {
+            XCTFail("Failed to construct Cmd+, event")
+            return
+        }
+
+#if DEBUG
+        XCTAssertTrue(
+            appDelegate.debugHandleCustomShortcut(event: event),
+            "Cmd+, should remain app-scoped when the key event comes from a non-terminal window"
+        )
+#else
+        XCTFail("debugHandleCustomShortcut is only available in DEBUG")
+#endif
+        XCTAssertEqual(settingsOpenCount, 1)
+    }
+
     func testCmdIStillTriggersShowNotificationsShortcut() {
         guard let appDelegate = AppDelegate.shared else {
             XCTFail("Expected AppDelegate.shared")