Cook the quinoa in the chicken stock. This can be done on the stovetop or in the instant pot.
When the squash is cooked, remove from the oven and using a fork, scrape the squash until you have lots of spaghetti. In a large bowl, combine the squash, sausage, mushrooms, onion, quinoa and nutritional yeast. Season with salt and pepper then add the mixture back to the squash boat. Top with cheese and return to the oven for 5 more minutes.