diff --git a/src/core/system.cpp b/src/core/system.cpp
index 7c67fe52b..91b02325d 100644
--- a/src/core/system.cpp
+++ b/src/core/system.cpp
@@ -930,7 +930,7 @@ void System::PauseSystem(bool paused)
   else
   {
     Host::OnSystemResumed();
-    g_host_display->SetVSync(ShouldUseVSync());
+    UpdateDisplaySync();
     ResetPerformanceCounters();
     ResetThrottler();
   }
@@ -1249,6 +1249,7 @@ bool System::Initialize(bool force_software_renderer)
   s_frame_number = 1;
   s_internal_frame_number = 1;
 
+  s_target_speed = g_settings.emulation_speed;
   s_throttle_frequency = 60.0f;
   s_frame_period = 0;
   s_next_frame_time = 0;
@@ -2064,30 +2065,7 @@ void System::ResetThrottler()
 
 void System::Throttle()
 {
-  // Allow variance of up to 40ms either way.
-#ifndef __ANDROID__
-  static constexpr double MAX_VARIANCE_TIME_NS = 40 * 1000000;
-#else
-  static constexpr double MAX_VARIANCE_TIME_NS = 50 * 1000000;
-#endif
-
-  // Use unsigned for defined overflow/wrap-around.
-  const Common::Timer::Value time = Common::Timer::GetCurrentValue();
-  const double sleep_time = (s_next_frame_time >= time) ?
-                              Common::Timer::ConvertValueToNanoseconds(s_next_frame_time - time) :
-                              -Common::Timer::ConvertValueToNanoseconds(time - s_next_frame_time);
-  if (sleep_time < -MAX_VARIANCE_TIME_NS)
-  {
-    // Don't display the slow messages in debug, it'll always be slow...
-#ifndef _DEBUG
-    Log_VerbosePrintf("System too slow, lost %.2f ms", (-sleep_time - MAX_VARIANCE_TIME_NS) / 1000000.0);
-#endif
-    ResetThrottler();
-  }
-  else
-  {
-    Common::Timer::SleepUntil(s_next_frame_time, true);
-  }
+  Common::Timer::SleepUntil(s_next_frame_time, true);
 }
 
 void System::RunFrames()
@@ -2210,12 +2188,7 @@ void System::UpdateSpeedLimiterState()
     }
   }
 
-  const bool video_sync_enabled = ShouldUseVSync();
-  const float max_display_fps = (!IsRunning() || m_throttler_enabled) ? 0.0f : g_settings.display_max_fps;
-  Log_InfoPrintf("Target speed: %f%%", target_speed * 100.0f);
-  Log_InfoPrintf("Using vsync: %s", video_sync_enabled ? "YES" : "NO");
-  Log_InfoPrintf("Max display fps: %f (%s)", max_display_fps,
-                 m_display_all_frames ? "displaying all frames" : "skipping displaying frames when needed");
+  Log_VerbosePrintf("Target speed: %f%%", s_target_speed * 100.0f);
 
   if (IsValid())
   {
@@ -2235,23 +2208,36 @@ void System::UpdateSpeedLimiterState()
     ResetThrottler();
   }
 
-  g_host_display->SetDisplayMaxFPS(max_display_fps);
-  g_host_display->SetVSync(video_sync_enabled);
+  // Defer vsync update until we unpause, in case of fullscreen UI.
+  if (IsRunning())
+    UpdateDisplaySync();
 
   if (g_settings.increase_timer_resolution)
     SetTimerResolutionIncreased(m_throttler_enabled);
 
   // When syncing to host and using vsync, we don't need to sleep.
-  if (syncing_to_host && video_sync_enabled && m_display_all_frames)
+  if (syncing_to_host && ShouldUseVSync() && m_display_all_frames)
   {
     Log_InfoPrintf("Using host vsync for throttling.");
     m_throttler_enabled = false;
   }
 }
 
+void System::UpdateDisplaySync()
+{
+  const bool video_sync_enabled = ShouldUseVSync();
+  const float max_display_fps = m_throttler_enabled ? 0.0f : g_settings.display_max_fps;
+  Log_VerbosePrintf("Using vsync: %s", video_sync_enabled ? "YES" : "NO");
+  Log_VerbosePrintf("Max display fps: %f (%s)", max_display_fps,
+    m_display_all_frames ? "displaying all frames" : "skipping displaying frames when needed");
+
+  g_host_display->SetDisplayMaxFPS(max_display_fps);
+  g_host_display->SetVSync(video_sync_enabled);
+}
+
 bool System::ShouldUseVSync()
 {
-  return (!IsRunning() || (m_throttler_enabled && g_settings.video_sync_enabled && !IsRunningAtNonStandardSpeed()));
+  return g_settings.video_sync_enabled && !IsRunningAtNonStandardSpeed();
 }
 
 bool System::IsFastForwardEnabled()
diff --git a/src/core/system.h b/src/core/system.h
index b32cc8ff5..0b4f522ab 100644
--- a/src/core/system.h
+++ b/src/core/system.h
@@ -230,6 +230,9 @@ void Throttle();
 void UpdatePerformanceCounters();
 void ResetPerformanceCounters();
 
+/// Resets vsync/max present fps state.
+void UpdateDisplaySync();
+
 // Access controllers for simulating input.
 Controller* GetController(u32 slot);
 void UpdateControllers();