Preheat the oven to 375ºF.
Add the onion, garlic, and quinoa to a casserole dish and toss the ingredients together.
Pour the butternut squash soup over the ingredients and stir to combine.
Add the salt, pepper, and chicken sausage and toss again. Be sure the quinoa is fully submerged in soup.
Submerge the thyme bundle into the middle of the casserole.
Cover and bake for 30 minutes.
Stir the casserole and cover again. Bake for an additional 30 minutes.
Finally, uncover the casserole and remove the bundle of thyme. Spread the cheese evenly over the top of the casserole. Turn the oven to broil and broil the cheese for 1-3 minutes (time may vary based on the oven) until melted and slightly browned.
Remove from the oven and let it rest for 10 minutes before serving.
Garnish with fresh thyme and enjoy.