Preheat oven to 400 Degrees F. Line a large baking sheet with aluminum foil.Set aside.
Cut 3 acorn squash in half and scoop out seeds and pulp with a spoon.
Coat the cavity of each squash with olive oil then season with salt and pepper to taste.
Place cavity side down on baking sheet and place in preheated oven on the middle rack. Bake for 45 minutes.
While squash is baking prepare stuffing.
Heat a tablespoon of oil in a large skillet over medium high heat.
Add chopped onions and celery and sautee for 3-5 minutes.
Add sausage. Cook and mix together with a wooden spoon, breaking up the sausage as it cooks. Cook for about 5-7 minutes.
Add apples, craisins, pecans, thyme and sage. Toss to combine with the sausage and cook for 2-3 more minutes.
Add cooked quinoa and toss to combine.
Remove skillet from heat and set aside until squash are finished cooking.
Once the squash is ready remove them from the oven. Carefully turn each over so that the cavity side is facing up. Fill each cavity with apple, sausage stuffing then top with shredded parmesan cheese.
Place back in oven for 10 minutes.
Remove from oven and serve.