Add cubed butternut squash and cook until fork tender, approximately 8-10 minutes.
Once cooked, transfer butternut squash out of boiling water to a blender. Add elbow macaroni noodles to the boiling water and cook until al-dente according to package instructions.
Add milk to the blender of butternut squash and blend until smooth.
Once noodles are fully cooked, drain and add back to pot. Add butternut squash mixture and cheeses and stir until fully combined. Season with salt and pepper.