diff --git a/Source/Core/DolphinQt2/Config/Graphics/GeneralWidget.cpp b/Source/Core/DolphinQt2/Config/Graphics/GeneralWidget.cpp
index a99ddfc9b14f..339049bd203d 100644
--- a/Source/Core/DolphinQt2/Config/Graphics/GeneralWidget.cpp
+++ b/Source/Core/DolphinQt2/Config/Graphics/GeneralWidget.cpp
@@ -165,7 +165,7 @@ void GeneralWidget::LoadSettings()
   // Render to Main Window
   m_render_main_window->setChecked(SConfig::GetInstance().bRenderToMain);
   // Keep Window on Top
-  m_keep_window_top->setChecked(SConfig::GetInstance().bKeepWindowOnTop);
+  m_keep_window_top->setChecked(Settings::Instance().IsKeepWindowOnTopEnabled());
   // Autoadjust Window size
   m_autoadjust_window_size->setChecked(SConfig::GetInstance().bRenderWindowAutoSize);
 }
@@ -222,7 +222,7 @@ void GeneralWidget::SaveSettings()
   // Render to Main Window
   SConfig::GetInstance().bRenderToMain = m_render_main_window->isChecked();
   // Keep Window on Top
-  SConfig::GetInstance().bKeepWindowOnTop = m_keep_window_top->isChecked();
+  Settings::Instance().SetKeepWindowOnTop(m_keep_window_top->isChecked());
   // Autoadjust windowsize
   SConfig::GetInstance().bRenderWindowAutoSize = m_autoadjust_window_size->isChecked();
 }
diff --git a/Source/Core/DolphinQt2/RenderWidget.cpp b/Source/Core/DolphinQt2/RenderWidget.cpp
index 255bff6cd70f..b1c1529baadc 100644
--- a/Source/Core/DolphinQt2/RenderWidget.cpp
+++ b/Source/Core/DolphinQt2/RenderWidget.cpp
@@ -53,6 +53,9 @@ RenderWidget::RenderWidget(QWidget* parent) : QWidget(parent)
   connect(&Settings::Instance(), &Settings::HideCursorChanged, this,
           &RenderWidget::OnHideCursorChanged);
   OnHideCursorChanged();
+  connect(&Settings::Instance(), &Settings::KeepWindowOnTopChanged, this,
+          &RenderWidget::OnKeepOnTopChanged);
+  OnKeepOnTopChanged(Settings::Instance().IsKeepWindowOnTopEnabled());
   m_mouse_timer->start(MOUSE_HIDE_DELAY);
 
   SetFillBackground(true);
@@ -70,6 +73,14 @@ void RenderWidget::OnHideCursorChanged()
   setCursor(Settings::Instance().GetHideCursor() ? Qt::BlankCursor : Qt::ArrowCursor);
 }
 
+void RenderWidget::OnKeepOnTopChanged(bool top)
+{
+  setWindowFlags(top ? windowFlags() | Qt::WindowStaysOnTopHint :
+                       windowFlags() & ~Qt::WindowStaysOnTopHint);
+
+  show();
+}
+
 void RenderWidget::HandleCursorTimer()
 {
   if (isActiveWindow())
@@ -90,6 +101,8 @@ bool RenderWidget::event(QEvent* event)
 {
   switch (event->type())
   {
+  case QEvent::Paint:
+    return !autoFillBackground();
   case QEvent::KeyPress:
   {
     QKeyEvent* ke = static_cast<QKeyEvent*>(event);
@@ -116,9 +129,13 @@ bool RenderWidget::event(QEvent* event)
     break;
   case QEvent::WindowActivate:
     Host::GetInstance()->SetRenderFocus(true);
+    if (SConfig::GetInstance().m_PauseOnFocusLost && Core::GetState() == Core::State::Paused)
+      Core::SetState(Core::State::Running);
     break;
   case QEvent::WindowDeactivate:
     Host::GetInstance()->SetRenderFocus(false);
+    if (SConfig::GetInstance().m_PauseOnFocusLost && Core::GetState() == Core::State::Running)
+      Core::SetState(Core::State::Paused);
     break;
   case QEvent::Resize:
   {
diff --git a/Source/Core/DolphinQt2/RenderWidget.h b/Source/Core/DolphinQt2/RenderWidget.h
index be276d10fc4f..0c89363fa042 100644
--- a/Source/Core/DolphinQt2/RenderWidget.h
+++ b/Source/Core/DolphinQt2/RenderWidget.h
@@ -29,6 +29,7 @@ class RenderWidget final : public QWidget
 private:
   void HandleCursorTimer();
   void OnHideCursorChanged();
+  void OnKeepOnTopChanged(bool top);
   void SetFillBackground(bool fill);
 
   static constexpr int MOUSE_HIDE_DELAY = 3000;
diff --git a/Source/Core/DolphinQt2/Settings.cpp b/Source/Core/DolphinQt2/Settings.cpp
index b697b8c43146..be4ca8001118 100644
--- a/Source/Core/DolphinQt2/Settings.cpp
+++ b/Source/Core/DolphinQt2/Settings.cpp
@@ -130,6 +130,20 @@ bool Settings::GetHideCursor() const
   return SConfig::GetInstance().bHideCursor;
 }
 
+void Settings::SetKeepWindowOnTop(bool top)
+{
+  if (IsKeepWindowOnTopEnabled() == top)
+    return;
+
+  SConfig::GetInstance().bKeepWindowOnTop = top;
+  emit KeepWindowOnTopChanged(top);
+}
+
+bool Settings::IsKeepWindowOnTopEnabled() const
+{
+  return SConfig::GetInstance().bKeepWindowOnTop;
+}
+
 int Settings::GetVolume() const
 {
   return SConfig::GetInstance().m_Volume;
diff --git a/Source/Core/DolphinQt2/Settings.h b/Source/Core/DolphinQt2/Settings.h
index 7e40803e1746..eea558546c5b 100644
--- a/Source/Core/DolphinQt2/Settings.h
+++ b/Source/Core/DolphinQt2/Settings.h
@@ -74,6 +74,8 @@ class Settings final : public QObject
   // Graphics
   void SetHideCursor(bool hide_cursor);
   bool GetHideCursor() const;
+  void SetKeepWindowOnTop(bool top);
+  bool IsKeepWindowOnTopEnabled() const;
 
   // Audio
   int GetVolume() const;
@@ -126,6 +128,7 @@ class Settings final : public QObject
   void DefaultGameChanged(const QString&);
   void PathReloadRequested(const QString&);
   void HideCursorChanged();
+  void KeepWindowOnTopChanged(bool top);
   void VolumeChanged(int volume);
   void NANDRefresh();
   void RegistersVisibilityChanged(bool visible);
diff --git a/Source/Core/DolphinQt2/Settings/InterfacePane.cpp b/Source/Core/DolphinQt2/Settings/InterfacePane.cpp
index 7e7fba1ceb73..d2b0e5084ad5 100644
--- a/Source/Core/DolphinQt2/Settings/InterfacePane.cpp
+++ b/Source/Core/DolphinQt2/Settings/InterfacePane.cpp
@@ -178,7 +178,7 @@ void InterfacePane::LoadConfig()
 {
   const SConfig& startup_params = SConfig::GetInstance();
   m_checkbox_auto_window->setChecked(startup_params.bRenderWindowAutoSize);
-  m_checkbox_top_window->setChecked(startup_params.bKeepWindowOnTop);
+  m_checkbox_top_window->setChecked(Settings::Instance().IsKeepWindowOnTopEnabled());
   m_checkbox_render_to_window->setChecked(startup_params.bRenderToMain);
   m_checkbox_use_builtin_title_database->setChecked(startup_params.m_use_builtin_title_database);
   m_checkbox_show_debugging_ui->setChecked(Settings::Instance().IsDebugModeEnabled());
@@ -200,7 +200,7 @@ void InterfacePane::OnSaveConfig()
 {
   SConfig& settings = SConfig::GetInstance();
   settings.bRenderWindowAutoSize = m_checkbox_auto_window->isChecked();
-  settings.bKeepWindowOnTop = m_checkbox_top_window->isChecked();
+  Settings::Instance().SetKeepWindowOnTop(m_checkbox_top_window->isChecked());
   settings.bRenderToMain = m_checkbox_render_to_window->isChecked();
   settings.m_use_builtin_title_database = m_checkbox_use_builtin_title_database->isChecked();
   Settings::Instance().SetDebugModeEnabled(m_checkbox_show_debugging_ui->isChecked());