diff --git a/src/citra_qt/bootmanager.cpp b/src/citra_qt/bootmanager.cpp
index 55a30d839..90b7ad40b 100644
--- a/src/citra_qt/bootmanager.cpp
+++ b/src/citra_qt/bootmanager.cpp
@@ -137,7 +137,6 @@ GRenderWindow::GRenderWindow(QWidget* parent, EmuThread* emu_thread) :
     NotifyClientAreaSizeChanged(std::pair<unsigned,unsigned>(child->width(), child->height()));
 
     BackupGeometry();
-
 }
 
 void GRenderWindow::moveContext()
@@ -287,11 +286,11 @@ void GRenderWindow::OnMinimalClientAreaChangeRequest(const std::pair<unsigned,un
 }
 
 void GRenderWindow::focusInEvent(QFocusEvent*) {
-    if (emu_thread && UISettings::values.pause_onfocuslost) emit gotFocus();
+    emit focusChanged(true);
 }
 
 void GRenderWindow::focusOutEvent(QFocusEvent*) {
-    if (emu_thread && UISettings::values.pause_onfocuslost) emit lostFocus();
+    emit focusChanged(false);
 }
 
 void GRenderWindow::OnEmulationStarting(EmuThread* emu_thread) {
diff --git a/src/citra_qt/bootmanager.h b/src/citra_qt/bootmanager.h
index c6113837e..6965f4256 100644
--- a/src/citra_qt/bootmanager.h
+++ b/src/citra_qt/bootmanager.h
@@ -136,10 +136,8 @@ public slots:
 signals:
     /// Emitted when the window is closed
     void Closed();
-    /// Emitted when the window got focus
-    void gotFocus();
-    /// Emitted when the window lost focus
-    void lostFocus();
+    /// Emitted when the window focus changed
+    void focusChanged(bool hasFocus);
 
 private:
     void OnMinimalClientAreaChangeRequest(const std::pair<unsigned,unsigned>& minimal_size) override;
diff --git a/src/citra_qt/main.cpp b/src/citra_qt/main.cpp
index a59553e40..7e87037b2 100644
--- a/src/citra_qt/main.cpp
+++ b/src/citra_qt/main.cpp
@@ -186,8 +186,7 @@ GMainWindow::GMainWindow() : config(new Config()), emu_thread(nullptr)
     connect(this, SIGNAL(EmulationStarting(EmuThread*)), graphicsTracingWidget, SLOT(OnEmulationStarting(EmuThread*)));
     connect(this, SIGNAL(EmulationStopping()), graphicsTracingWidget, SLOT(OnEmulationStopping()));
 
-    connect(render_window, SIGNAL(gotFocus()), this, SLOT(OnStartGame()));
-    connect(render_window, SIGNAL(lostFocus()), this, SLOT(OnPauseGame()));
+    connect(render_window, SIGNAL(focusChanged(bool)), this, SLOT(OnFocusChanged(bool)));
 
     // Setup hotkeys
     RegisterHotkey("Main Window", "Load File", QKeySequence::Open);
@@ -472,6 +471,8 @@ void GMainWindow::OnStartGame() {
     ui.action_Stop->setEnabled(true);
 
     render_window->setFocus();
+
+    emulation_paused = false;
 }
 
 void GMainWindow::OnPauseGame() {
@@ -480,12 +481,30 @@ void GMainWindow::OnPauseGame() {
     ui.action_Start->setEnabled(true);
     ui.action_Pause->setEnabled(false);
     ui.action_Stop->setEnabled(true);
+
+    emulation_paused = true;
 }
 
 void GMainWindow::OnStopGame() {
     ShutdownGame();
 }
 
+void GMainWindow::OnFocusChanged(bool hasFocus) {
+    // The focus change does not impact actual emulator state if:
+    // - the option is disabled
+    // - the emulation is not started
+    // - the emulation has been paused through menu
+    if(!UISettings::values.pause_onfocuslost ||
+       !emu_thread ||
+       emulation_paused)
+        return;
+
+    if (hasFocus)
+        emu_thread->SetRunning(true);
+    else // focus lost
+        emu_thread->SetRunning(false);
+}
+
 void GMainWindow::ToggleWindowMode() {
     if (ui.action_Single_Window_Mode->isChecked()) {
         // Render in the main window...
@@ -521,6 +540,10 @@ void GMainWindow::OnConfigure() {
         render_window->ReloadSetKeymaps();
         config->Save();
     }
+
+    // Make sure the emulation is running when all pauses are disabled
+    if (emu_thread && !UISettings::values.pause_onfocuslost && !emulation_paused)
+        emu_thread->SetRunning(true);
 }
 
 void GMainWindow::OnCreateGraphicsSurfaceViewer() {
diff --git a/src/citra_qt/main.h b/src/citra_qt/main.h
index b836b13fb..7893102c0 100644
--- a/src/citra_qt/main.h
+++ b/src/citra_qt/main.h
@@ -98,6 +98,8 @@ private slots:
     void OnStartGame();
     void OnPauseGame();
     void OnStopGame();
+    /// Called whenever the render window focus is changed
+    void OnFocusChanged(bool hasFocus);
     /// Called whenever a user selects a game in the game list widget.
     void OnGameListLoadFile(QString game_path);
     void OnMenuLoadFile();
@@ -118,6 +120,8 @@ private:
 
     std::unique_ptr<Config> config;
 
+    // Whether emulation has been paused (through menus)
+    bool emulation_paused = false;
     // Whether emulation is currently running in Citra.
     bool emulation_running = false;
     std::unique_ptr<EmuThread> emu_thread;