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Heat oven to 350 F.
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Heat a skillet over medium-high heat. Add the beef and onions and cook, stirring frequently to break up meat, until no longer pink, 7 to 8 minutes. Drain excess fat. Stir in ¾ cup enchilada sauce.
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Pour 1 ⅓ cups enchilada sauce into 9x13 baking dish, spreading it evenly. Arrange 6 tortillas, slightly overlapping, to cover the bottom of the baking dish.
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Spoon half of the beef mixture on top, followed by half of the beans, half of the chiles and 1 ⅓ cups cheddar.
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Arrange 6 tortillas on top, followed by 1 cup enchilada sauce, then remaining beef, beans, chiles and 1 ⅓ cups cheddar.
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Top with remaining 6 tortillas on top and remaining sauce.
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Cover with aluminum foil and bake for 50 minutes. Remove foil and sprinkle the remaining 1 ⅓ cups cheddar on top.
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Bake until heated through and cheese is melted, 10 to 15 minutes. Let sit 10 minutes, top with black olives, cotija and cilantro.