Preheat the oven to 400°.
Halve the butternut squash & place on a baking sheet, flesh side down. Bake in the oven for 45-55 minutes or until fork tender.
Meanwhile, prepare the filling. Finely chop the onion and garlic and roughly chop the mushrooms.
In a large pot over medium-high heat, saute the onion and garlic for 2-3 minutes, until slightly softened. Add the mushrooms and saute for another 2 minutes.
Add pinto beans, tomatoes, and spices to the pot. Cover and bring to a boil, then lower to simmer for 15 minutes. Turn off the heat and leave it covered until the butternut squash is done (you'll want it to stay warm when ready to stuff the squash).
Season with salt and pepper.
Once the butternut squash is done, take it out of the oven, scoop out the seeds and discard them. Then scoop out most of the flesh, add it to the filling, and mix until combined.
Stuff the filling into the squash halves and serve.