diff --git a/GPU/D3D11/GPU_D3D11.cpp b/GPU/D3D11/GPU_D3D11.cpp
index 091c10a946..342f033738 100644
--- a/GPU/D3D11/GPU_D3D11.cpp
+++ b/GPU/D3D11/GPU_D3D11.cpp
@@ -163,6 +163,7 @@ void GPU_D3D11::BeginFrame() {
 		// This most likely means that saw equal depth changed.
 		WARN_LOG(G3D, "Shader use flags changed, clearing all shaders");
 		shaderManagerD3D11_->ClearShaders();
+		drawEngine_.ClearInputLayoutMap();
 		gstate_c.useFlagsChanged = false;
 	}
 }