Bring water and quinoa to a boil in a saucepan. Reduce heat to medium-low, cover, and simmer until quinoa is tender, 15 to 20 minutes.
Preheat the oven to 350 degrees F (175 degrees C).
Heat oil in a skillet over medium-high heat. Saute green bell peppers and onion until softened, 5 to 7 minutes.
Mix chicken breasts, black beans, tomatoes, cream of chicken soup, half the Cheddar cheese, sour cream, chili powder, and cayenne pepper together in a bowl.
Place 1/2 the tortillas in the bottom of a baking pan. Spoon half the chicken mixture on top. Add the remaining tortillas and top with remaining chicken mixture. Sprinkle remaining Cheddar cheese on top.
Bake in the preheated oven until set, about 45 minutes.