diff --git a/gtk/src/gtk_s9xwindow.cpp b/gtk/src/gtk_s9xwindow.cpp
index cf8a13ba..cae3fdd2 100644
--- a/gtk/src/gtk_s9xwindow.cpp
+++ b/gtk/src/gtk_s9xwindow.cpp
@@ -520,7 +520,7 @@ void Snes9xWindow::focus_notify(bool state)
 {
     focused = state;
 
-    if (!state && config->pause_emulation_on_switch)
+    if (!state && config->pause_emulation_on_switch && !paused_from_focus_loss)
     {
         sys_pause++;
         propagate_pause_state();