diff --git a/src/core/system.cpp b/src/core/system.cpp
index f2318e123..dd2b08862 100644
--- a/src/core/system.cpp
+++ b/src/core/system.cpp
@@ -445,8 +445,6 @@ void System::RunFrame()
 
   // Generate any pending samples from the SPU before sleeping, this way we reduce the chances of underruns.
   m_spu->GeneratePendingSamples();
-
-  UpdatePerformanceCounters();
 }
 
 void System::SetThrottleFrequency(float frequency)
diff --git a/src/duckstation-qt/qthostinterface.cpp b/src/duckstation-qt/qthostinterface.cpp
index 0fcb791d1..f6b0c3757 100644
--- a/src/duckstation-qt/qthostinterface.cpp
+++ b/src/duckstation-qt/qthostinterface.cpp
@@ -735,6 +735,8 @@ void QtHostInterface::threadEntryPoint()
 
     renderDisplay();
 
+    m_system->UpdatePerformanceCounters();
+
     if (m_speed_limiter_enabled)
       m_system->Throttle();
 
diff --git a/src/duckstation-sdl/sdl_host_interface.cpp b/src/duckstation-sdl/sdl_host_interface.cpp
index 8c9745610..03a56359c 100644
--- a/src/duckstation-sdl/sdl_host_interface.cpp
+++ b/src/duckstation-sdl/sdl_host_interface.cpp
@@ -1438,6 +1438,7 @@ void SDLHostInterface::Run()
       if (m_system)
       {
         m_system->GetGPU()->RestoreGraphicsAPIState();
+        m_system->UpdatePerformanceCounters();
 
         if (m_speed_limiter_enabled)
           m_system->Throttle();