Preheat oven to 350°F (175°C) and spray a baking dish with nonstick cooking spray.
In a mixing bowl, whisk together eggs, milk, salt, and pepper until well combined.
Place tortillas flat into the greased baking dish, slightly overlapping to cover the bottom.
Sprinkle half of the cheese, bacon (or sausage), bell peppers, and green onions over the tortillas.
Pour the egg mixture evenly over the ingredients.
Top with the remaining cheese and toppings.
Bake for 25-30 minutes or until the eggs are fully set and the top is golden.
Let cool slightly before slicing. Serve warm.