diff --git a/Source/Core/DolphinQt/Host.cpp b/Source/Core/DolphinQt/Host.cpp
index 46b0aa8963a..78ff0fae8a8 100644
--- a/Source/Core/DolphinQt/Host.cpp
+++ b/Source/Core/DolphinQt/Host.cpp
@@ -108,7 +108,7 @@ static void RunWithGPUThreadInactive(std::function<void()> f)
     auto& fifo = system.GetFifo();
     fifo.PauseAndLock(true, was_running);
     f();
-    fifo.PauseAndLock(false, was_running);
+    fifo.RestoreState(was_running);
   }
   else
   {
diff --git a/Source/Core/VideoCommon/Fifo.cpp b/Source/Core/VideoCommon/Fifo.cpp
index 513b6554087..7e07e0bbf37 100644
--- a/Source/Core/VideoCommon/Fifo.cpp
+++ b/Source/Core/VideoCommon/Fifo.cpp
@@ -86,6 +86,12 @@ void FifoManager::PauseAndLock(bool do_lock, bool unpause_on_unlock)
   }
 }
 
+void FifoManager::RestoreState(const bool was_running)
+{
+  if (was_running)
+    EmulatorState(true);
+}
+
 void FifoManager::Init()
 {
   if (!m_config_callback_id)
diff --git a/Source/Core/VideoCommon/Fifo.h b/Source/Core/VideoCommon/Fifo.h
index 2fce8fdcb53..c6fc6376615 100644
--- a/Source/Core/VideoCommon/Fifo.h
+++ b/Source/Core/VideoCommon/Fifo.h
@@ -53,6 +53,7 @@ public:
   void Prepare();  // Must be called from the CPU thread.
   void DoState(PointerWrap& f);
   void PauseAndLock(bool do_lock, bool unpause_on_unlock);
+  void RestoreState(bool was_running);
   void UpdateWantDeterminism(bool want);
   bool UseDeterministicGPUThread() const { return m_use_deterministic_gpu_thread; }
   bool UseSyncGPU() const { return m_config_sync_gpu; }
diff --git a/Source/Core/VideoCommon/VideoConfig.cpp b/Source/Core/VideoCommon/VideoConfig.cpp
index 46f8732c2fa..4c11fb084e8 100644
--- a/Source/Core/VideoCommon/VideoConfig.cpp
+++ b/Source/Core/VideoCommon/VideoConfig.cpp
@@ -70,7 +70,7 @@ void VideoConfig::Refresh()
       g_Config.VerifyValidity();
 
       if (lock_gpu_thread)
-        system.GetFifo().PauseAndLock(false, true);
+        system.GetFifo().RestoreState(true);
     };
 
     s_config_changed_callback_id =