diff --git a/pcsx2/gui/AppCoreThread.cpp b/pcsx2/gui/AppCoreThread.cpp
index a34268cf48..e84ee0600b 100644
--- a/pcsx2/gui/AppCoreThread.cpp
+++ b/pcsx2/gui/AppCoreThread.cpp
@@ -510,6 +510,9 @@ void AppCoreThread::ApplySettings( const Pcsx2Config& src )
 	{
 		_parent::ApplySettings( fixup );
 	}
+
+	if (m_ExecMode >= ExecMode_Paused)
+		GSsetVsync(EmuConfig.GS.FrameLimitEnable ? EmuConfig.GS.GetVsync() : 0);
 }
 
 // --------------------------------------------------------------------------------------
diff --git a/pcsx2/gui/GlobalCommands.cpp b/pcsx2/gui/GlobalCommands.cpp
index 5be6ece48c..30a1c84ed6 100644
--- a/pcsx2/gui/GlobalCommands.cpp
+++ b/pcsx2/gui/GlobalCommands.cpp
@@ -122,8 +122,6 @@ namespace Implementations
 
 		gsUpdateFrequency(g_Conf->EmuOptions);
 
-		GSsetVsync(g_Conf->EmuOptions.GS.GetVsync());
-
 		pauser.AllowResume();
 	}
 
@@ -150,8 +148,6 @@ namespace Implementations
 
 		gsUpdateFrequency(g_Conf->EmuOptions);
 
-		GSsetVsync(g_Conf->EmuOptions.GS.GetVsync());
-
 		pauser.AllowResume();
 	}
 
@@ -164,12 +160,6 @@ namespace Implementations
 		// Turbo/Slowmo don't make sense when framelimiter is toggled
 		g_LimiterMode = Limit_Nominal;
 
-		// Disable Vsync when frame limited is disabled
-		if( g_Conf->EmuOptions.GS.FrameLimitEnable )
-			GSsetVsync(g_Conf->EmuOptions.GS.GetVsync());
-		else
-			GSsetVsync(0);
-
 		pauser.AllowResume();
 	}