Cut spaghetti squash in half, lengthwise, and scrape out seeds and filling.
Place cut side down on an oiled baking sheet. Bake for 20-30 minutes.
Toss chicken into an oiled saute pan on medium-high heat. Cook for 4 minutes then add the red peppers, making sure not to overcook the chicken (you want it to be 3/4 the way done because the chicken will cook more in the oven).
Once spaghetti squash is roasted, remove it from the oven and carefully scrape out the insides, the “spaghetti squash noodles,” into a bowl, and save the squash shell halves.
Add the enchilada sauce, the chicken, and the peppers to the bowl, and mix. Once mixed, fill in the squash shells with the mixture and sprinkle the cheese on top. Put back into the oven and cook an additional 15 minutes.