diff --git a/src/apprt/gtk/App.zig b/src/apprt/gtk/App.zig
index 6c506817b..9a9c2fb41 100644
--- a/src/apprt/gtk/App.zig
+++ b/src/apprt/gtk/App.zig
@@ -16,6 +16,7 @@ const builtin = @import("builtin");
 const glfw = @import("glfw");
 const configpkg = @import("../../config.zig");
 const input = @import("../../input.zig");
+const internal_os = @import("../../os/main.zig");
 const Config = configpkg.Config;
 const CoreApp = @import("../../App.zig");
 const CoreSurface = @import("../../Surface.zig");
@@ -72,10 +73,16 @@ pub fn init(core_app: *CoreApp, opts: Options) !App {
     const cursor_none = c.gdk_cursor_new_from_name("none", null);
     errdefer if (cursor_none) |cursor| c.g_object_unref(cursor);
 
+    const single_instance = switch (config.@"gtk-single-instance") {
+        .true => true,
+        .false => false,
+        .desktop => internal_os.launchedFromDesktop(),
+    };
+
     // Setup the flags for our application.
     const app_flags: c.GApplicationFlags = app_flags: {
         var flags: c.GApplicationFlags = c.G_APPLICATION_DEFAULT_FLAGS;
-        if (!config.@"gtk-single-instance") flags |= c.G_APPLICATION_NON_UNIQUE;
+        if (!single_instance) flags |= c.G_APPLICATION_NON_UNIQUE;
         break :app_flags flags;
     };
 
@@ -88,6 +95,10 @@ pub fn init(core_app: *CoreApp, opts: Options) !App {
     };
 
     // Create our GTK Application which encapsulates our process.
+    log.debug("creating GTK application id={s} single-instance={}", .{
+        app_id,
+        single_instance,
+    });
     const app = @as(?*c.GtkApplication, @ptrCast(c.gtk_application_new(
         app_id.ptr,
         app_flags,
diff --git a/src/config/Config.zig b/src/config/Config.zig
index 6d42516b6..1b6e8d84b 100644
--- a/src/config/Config.zig
+++ b/src/config/Config.zig
@@ -406,14 +406,19 @@ keybind: Keybinds = .{},
 /// This does not work with GLFW builds.
 @"macos-option-as-alt": OptionAsAlt = .false,
 
-/// If true (default), then the Ghostty GTK application will run in
-/// single-instance mode: each new `ghostty` process launched will result
-/// in a new window, if there is already a running process.
+/// If true, the Ghostty GTK application will run in single-instance mode:
+/// each new `ghostty` process launched will result in a new window if there
+/// is already a running process.
 ///
 /// If false, each new ghostty process will launch a separate application.
 ///
-/// Debug builds of Ghostty have a separate single-instance ID.
-@"gtk-single-instance": bool = true,
+/// The default value is "desktop" which will default to "true" if Ghostty
+/// detects it was launched from the .desktop file such as an app launcher.
+/// If Ghostty is launched from the command line, it will default to "false".
+///
+/// Note that debug builds of Ghostty have a separate single-instance ID
+/// so you can test single instance without conflicting with release builds.
+@"gtk-single-instance": GtkSingleInstance = .desktop,
 
 /// If true (default), then the Ghostty GTK tabs will be "wide." Wide tabs
 /// are the new typical Gnome style where tabs fill their available space.
@@ -1856,3 +1861,10 @@ pub const WindowTheme = enum {
     light,
     dark,
 };
+
+/// See gtk-single-instance
+pub const GtkSingleInstance = enum {
+    desktop,
+    false,
+    true,
+};