diff --git a/src/citra_qt/main.cpp b/src/citra_qt/main.cpp
index 0fc10508e..a401ce2d9 100644
--- a/src/citra_qt/main.cpp
+++ b/src/citra_qt/main.cpp
@@ -503,9 +503,11 @@ void GMainWindow::OnLoseFocus(Qt::ApplicationState state) {
     if (ui.action_Pause->isEnabled() &&
         (state == Qt::ApplicationSuspended ||
          state & (Qt::ApplicationHidden | Qt::ApplicationInactive))) {
+        auto_paused = true;
         OnPauseGame();
     }
-    if (ui.action_Start->isEnabled() && state == Qt::ApplicationActive) {
+    if (ui.action_Start->isEnabled() && auto_paused && state == Qt::ApplicationActive) {
+        auto_paused = false;
         OnStartGame();
     }
 }
diff --git a/src/citra_qt/main.h b/src/citra_qt/main.h
index 82c94972c..9cb6886d3 100644
--- a/src/citra_qt/main.h
+++ b/src/citra_qt/main.h
@@ -233,6 +233,8 @@ private:
     // The path to the game currently running
     QString game_path;
 
+    bool auto_paused = false;
+
     // Movie
     bool movie_record_on_start = false;
     QString movie_record_path;