Preheat oven to 400F.
Peel and cube butternut squash, flesh removed. Toss with 2 teaspoon olive oil, salt and pepper to taste. Place on parchment paper or foil lined baking sheet, and bake for about 30 minutes, until easily pierced with a fork.
While butternut squash is baking, heat 2 teaspoon olive oil in a pan on medium heat. Add in onion, garlic, and mushrooms. Sauté for about 5 minutes, until onion is translucent. Then add in spinach, stirring until wilted. Remove from heat.
When butternut squash is done baking, remove from oven and place in a large bowl. Mash the squash with the back of a large fork. Then, mix in the mushroom mixture until evenly distributed.
Mix in the cooked quinoa, diced green chilis, cumin, chili powder, and smoked paprika. Salt and pepper to taste.
In a 9x13 baking dish, spread ½ cup of enchilada sauce on the bottom.
Place 2 heaping spoonfuls of filling in a tortilla, wrapping tightly and placing seam side down on baking dish. Repeat until filling is gone.
Top with remaining enchilada sauce and shredded cheese.
Place enchiladas in oven for about 20 minutes, until cheese is melted and golden brown.
Remove from oven, serve, and enjoy!