diff --git a/Source/Core/VideoBackends/D3D/D3DUtil.cpp b/Source/Core/VideoBackends/D3D/D3DUtil.cpp
index 89bdbcee97..28b9850902 100644
--- a/Source/Core/VideoBackends/D3D/D3DUtil.cpp
+++ b/Source/Core/VideoBackends/D3D/D3DUtil.cpp
@@ -10,6 +10,7 @@
 #include "VideoBackends/D3D/D3DShader.h"
 #include "VideoBackends/D3D/D3DState.h"
 #include "VideoBackends/D3D/D3DUtil.h"
+#include "VideoBackends/D3D/GeometryShaderCache.h"
 #include "VideoBackends/D3D/PixelShaderCache.h"
 #include "VideoBackends/D3D/VertexShaderCache.h"
 
@@ -653,6 +654,7 @@ void drawColorQuad(u32 Color, float x1, float y1, float x2, float y2)
 	}
 
 	stateman->SetVertexShader(VertexShaderCache::GetClearVertexShader());
+	stateman->SetGeometryShader(g_ActiveConfig.iStereoMode > 0 ? GeometryShaderCache::GetClearGeometryShader() : nullptr);
 	stateman->SetPixelShader(PixelShaderCache::GetClearProgram());
 	stateman->SetInputLayout(VertexShaderCache::GetClearInputLayout());
 
@@ -663,9 +665,11 @@ void drawColorQuad(u32 Color, float x1, float y1, float x2, float y2)
 
 	stateman->Apply();
 	context->Draw(4, cq_offset);
+
+	stateman->SetGeometryShader(nullptr);
 }
 
-void drawClearQuad(u32 Color, float z, ID3D11PixelShader* PShader, ID3D11VertexShader* Vshader, ID3D11InputLayout* layout)
+void drawClearQuad(u32 Color, float z)
 {
 	ClearVertex coords[4] = {
 		{-1.0f,  1.0f, z, Color},
@@ -683,9 +687,10 @@ void drawClearQuad(u32 Color, float z, ID3D11PixelShader* PShader, ID3D11VertexS
 		clear_quad_data.z = z;
 	}
 
-	stateman->SetVertexShader(Vshader);
-	stateman->SetPixelShader(PShader);
-	stateman->SetInputLayout(layout);
+	stateman->SetVertexShader(VertexShaderCache::GetClearVertexShader());
+	stateman->SetGeometryShader(g_ActiveConfig.iStereoMode > 0 ? GeometryShaderCache::GetClearGeometryShader() : nullptr);
+	stateman->SetPixelShader(PixelShaderCache::GetClearProgram());
+	stateman->SetInputLayout(VertexShaderCache::GetClearInputLayout());
 
 	UINT stride = sizeof(ClearVertex);
 	UINT offset = 0;
@@ -694,6 +699,8 @@ void drawClearQuad(u32 Color, float z, ID3D11PixelShader* PShader, ID3D11VertexS
 
 	stateman->Apply();
 	context->Draw(4, clearq_offset);
+
+	stateman->SetGeometryShader(nullptr);
 }
 
 }  // namespace D3D
diff --git a/Source/Core/VideoBackends/D3D/D3DUtil.h b/Source/Core/VideoBackends/D3D/D3DUtil.h
index 53706847c2..0f2dd72adb 100644
--- a/Source/Core/VideoBackends/D3D/D3DUtil.h
+++ b/Source/Core/VideoBackends/D3D/D3DUtil.h
@@ -74,7 +74,7 @@ namespace D3D
 							ID3D11InputLayout* layout,
 							float Gamma = 1.0f,
 							u32 slice = 0);
-	void drawClearQuad(u32 Color, float z, ID3D11PixelShader* PShader, ID3D11VertexShader* Vshader, ID3D11InputLayout* layout);
+	void drawClearQuad(u32 Color, float z);
 	void drawColorQuad(u32 Color, float x1, float y1, float x2, float y2);
 }
 
diff --git a/Source/Core/VideoBackends/D3D/GeometryShaderCache.cpp b/Source/Core/VideoBackends/D3D/GeometryShaderCache.cpp
index a7bc1a470e..087428a200 100644
--- a/Source/Core/VideoBackends/D3D/GeometryShaderCache.cpp
+++ b/Source/Core/VideoBackends/D3D/GeometryShaderCache.cpp
@@ -27,8 +27,12 @@ const GeometryShaderCache::GSCacheEntry* GeometryShaderCache::last_entry;
 GeometryShaderUid GeometryShaderCache::last_uid;
 UidChecker<GeometryShaderUid,ShaderCode> GeometryShaderCache::geometry_uid_checker;
 
+ID3D11GeometryShader* ClearGeometryShader = nullptr;
+
 LinearDiskCache<GeometryShaderUid, u8> g_gs_disk_cache;
 
+ID3D11GeometryShader* GeometryShaderCache::GetClearGeometryShader() { return ClearGeometryShader; }
+
 ID3D11Buffer* gscbuf = nullptr;
 
 // this class will load the precompiled shaders into our cache
@@ -41,8 +45,43 @@ public:
 	}
 };
 
+const char clear_shader_code[] = {
+	"struct VSOUTPUT\n"
+	"{\n"
+	"float4 vPosition   : POSITION;\n"
+	"float4 vColor0   : COLOR0;\n"
+	"};\n"
+	"struct GSOUTPUT\n"
+	"{\n"
+	"float4 vPosition   : POSITION;\n"
+	"float4 vColor0   : COLOR0;\n"
+	"uint slice    : SV_RenderTargetArrayIndex;\n"
+	"};\n"
+	"[maxvertexcount(6)]\n"
+	"void main(triangle VSOUTPUT o[3], inout TriangleStream<GSOUTPUT> Output)\n"
+	"{\n"
+	"for(int slice = 0; slice < 2; slice++)\n"
+	"{\n"
+	"for(int i = 0; i < 3; i++)\n"
+	"{\n"
+	"GSOUTPUT OUT;\n"
+	"OUT.vPosition = o[i].vPosition;\n"
+	"OUT.vColor0 = o[i].vColor0;\n"
+	"OUT.slice = slice;\n"
+	"Output.Append(OUT);\n"
+	"}\n"
+	"Output.RestartStrip();\n"
+	"}\n"
+	"}\n"
+};
+
 void GeometryShaderCache::Init()
 {
+	// used when drawing clear quads
+	ClearGeometryShader = D3D::CompileAndCreateGeometryShader(clear_shader_code);
+	CHECK(ClearGeometryShader != nullptr, "Create clear geometry shader");
+	D3D::SetDebugObjectName((ID3D11DeviceChild*)ClearGeometryShader, "clear geometry shader");
+
 	Clear();
 
 	if (!File::Exists(File::GetUserPath(D_SHADERCACHE_IDX)))
@@ -72,6 +111,8 @@ void GeometryShaderCache::Clear()
 
 void GeometryShaderCache::Shutdown()
 {
+	SAFE_RELEASE(ClearGeometryShader);
+
 	Clear();
 	g_gs_disk_cache.Sync();
 	g_gs_disk_cache.Close();
diff --git a/Source/Core/VideoBackends/D3D/GeometryShaderCache.h b/Source/Core/VideoBackends/D3D/GeometryShaderCache.h
index b200323be8..38a524c596 100644
--- a/Source/Core/VideoBackends/D3D/GeometryShaderCache.h
+++ b/Source/Core/VideoBackends/D3D/GeometryShaderCache.h
@@ -21,6 +21,8 @@ public:
 	static bool SetShader(u32 components); // TODO: Should be renamed to LoadShader
 	static bool InsertByteCode(const GeometryShaderUid &uid, const void* bytecode, unsigned int bytecodelen);
 
+	static ID3D11GeometryShader* GeometryShaderCache::GetClearGeometryShader();
+
 	static ID3D11GeometryShader* GetActiveShader() { return last_entry->shader; }
 
 private:
diff --git a/Source/Core/VideoBackends/D3D/Render.cpp b/Source/Core/VideoBackends/D3D/Render.cpp
index 0cd5835b60..3d0b365242 100644
--- a/Source/Core/VideoBackends/D3D/Render.cpp
+++ b/Source/Core/VideoBackends/D3D/Render.cpp
@@ -547,7 +547,7 @@ void Renderer::ClearScreen(const EFBRectangle& rc, bool colorEnable, bool alphaE
 
 	// Color is passed in bgra mode so we need to convert it to rgba
 	u32 rgbaColor = (color & 0xFF00FF00) | ((color >> 16) & 0xFF) | ((color << 16) & 0xFF0000);
-	D3D::drawClearQuad(rgbaColor, (z & 0xFFFFFF) / float(0xFFFFFF), PixelShaderCache::GetClearProgram(), VertexShaderCache::GetClearVertexShader(), VertexShaderCache::GetClearInputLayout());
+	D3D::drawClearQuad(rgbaColor, (z & 0xFFFFFF) / float(0xFFFFFF));
 
 	D3D::stateman->PopDepthState();
 	D3D::stateman->PopBlendState();