Preheat the oven to 350 degrees.
In a large pan, sauté the pepper and onion over medium heat until translucent or about 5-8 minutes. Sprinkle half the salt and pepper over the pepper and onion while cooking.
Reduce the heat to medium-low. Add the black beans, tomatoes, chilies, garlic, spices and the rest of the salt and pepper to the pan. Stir the mixture together well and allow to simmer for 5-10 minutes, stirring occasionally. Taste and adjust spices if necessary.
Line the bottom of a greased 8x8 casserole dish with tortillas.
Layer ⅓ of the beans mixture on top of the tortillas.
Cover with ¼ of the cheese.
Repeat the layering another two times until you have three layers.
To finish the dish add another layer of tortillas. Cover that with the salsa and then the last quarter of the cheese.
Cover with foil and bake for 15 minutes.
Remove the foil and finish in the over for another 15 minutes. Total of 30 minutes in the oven.