Cut the top off the squash and scoop out the seeds. Microwave squash, cut side down in a dish with 1 inch of water for 12-15 minutes.
Brown sausage in a skillet over medium heat, then put the sausage in a bowl.
Pour off the sausage drippings, and then add the onions, carrots, mushrooms, green pepper and garlic to the skillet. Cook for 10 minutes, and then add to the sausage in the bowl.
Add the quinoa, cheese, salt and pepper to the sausage mix.
At this point you can refrigerate the squash and stuffing until you are ready to cook it. Or you can bake it right away.
Preheat the oven to 350. Stuff the squash with the filling, packing it down to fill the squash. Bake 30 minutes until it is heated through. You can also top with extra cheese if you like.