Preheat the oven to 375°F.
In a casserole dish, combine the minced onion, garlic, and quinoa. Mix them together.
Pour the butternut squash soup over the ingredients and stir until well combined.
Add the salt, pepper, and chopped chicken sausage, ensuring the quinoa is fully submerged in the soup.
Place the thyme bundle in the middle of the casserole.
Cover the dish and bake for 30 minutes.
After 30 minutes, stir the casserole, cover it again, and bake for another 30 minutes.
Uncover the casserole, remove the thyme bundle, and spread the shredded cheese evenly over the top.
Turn the oven to broil and broil the cheese for 1-3 minutes until melted and slightly browned.
Remove from the oven and let it cool for 10 minutes before serving.
Garnish with fresh thyme and enjoy!