Preheat the oven to 350 degrees Fahrenheit.
Grease a square glass baking dish with vegetable spray.
In a skillet, cook the chorizo. When nearly done, add the onions and sauté until cooked through.
Slice the chilies lengthwise, open them up, and remove any seeds and membranes.
Create a layer at the bottom of the baking dish using half of the chilies.
In a mixing bowl, whisk together the beaten eggs, salt, and black pepper.
Sprinkle half of the chorizo mixture over the layered chilies, followed by half of the finely chopped cheese.
Pour half of the beaten eggs over the top as the next layer.
Create another layer using the remaining chilies.
Repeat the layering process with the remaining chorizo and cheese, just as before.
Pour the remaining beaten eggs over the top layer.
Bake the casserole for approximately 30 to 40 minutes, or until a toothpick inserted in the center comes out clean.
Once baked, allow the casserole to cool for about 5 minutes.
Cut it into sections and serve with salsa poured over the top, alongside warm flour tortillas.