diff --git a/Source/Core/VideoBackends/OGL/Render.cpp b/Source/Core/VideoBackends/OGL/Render.cpp
index 802a1b1f96..1a0b7e5708 100644
--- a/Source/Core/VideoBackends/OGL/Render.cpp
+++ b/Source/Core/VideoBackends/OGL/Render.cpp
@@ -89,6 +89,8 @@ static RasterFont* s_pfont = nullptr;
 static int s_MSAASamples = 1;
 static int s_LastMultisampleMode = 0;
 
+static bool s_LastStereo = false;
+
 static u32 s_blendMode;
 
 static bool s_vsync;
@@ -591,6 +593,7 @@ Renderer::Renderer()
 	s_LastMultisampleMode = g_ActiveConfig.iMultisampleMode;
 	s_MSAASamples = GetNumMSAASamples(s_LastMultisampleMode);
 	ApplySSAASettings();
+	s_LastStereo = g_ActiveConfig.bStereo;
 
 	// Decide framebuffer size
 	s_backbuffer_width = (int)GLInterface->GetBackBufferWidth();
@@ -1690,15 +1693,16 @@ void Renderer::SwapImpl(u32 xfbAddr, u32 fbWidth, u32 fbStride, u32 fbHeight, co
 		s_LastEFBScale = g_ActiveConfig.iEFBScale;
 	}
 
-	if (xfbchanged || WindowResized || (s_LastMultisampleMode != g_ActiveConfig.iMultisampleMode))
+	if (xfbchanged || WindowResized || (s_LastMultisampleMode != g_ActiveConfig.iMultisampleMode) || (s_LastStereo != g_ActiveConfig.bStereo))
 	{
 		UpdateDrawRectangle(s_backbuffer_width, s_backbuffer_height);
 
-		if (CalculateTargetSize(s_backbuffer_width, s_backbuffer_height) || s_LastMultisampleMode != g_ActiveConfig.iMultisampleMode)
+		if (CalculateTargetSize(s_backbuffer_width, s_backbuffer_height) || s_LastMultisampleMode != g_ActiveConfig.iMultisampleMode || s_LastStereo != g_ActiveConfig.bStereo)
 		{
 			s_LastMultisampleMode = g_ActiveConfig.iMultisampleMode;
 			s_MSAASamples = GetNumMSAASamples(s_LastMultisampleMode);
 			ApplySSAASettings();
+			s_LastStereo = g_ActiveConfig.bStereo;
 
 			delete g_framebuffer_manager;
 			g_framebuffer_manager = new FramebufferManager(s_target_width, s_target_height,