Preheat the oven to 375°F (190°C).
In a large skillet over medium heat, cook the ground beef, diced onion, and minced garlic until the beef is browned and the onion is softened, about 7-8 minutes. Drain excess fat.
Stir in the enchilada sauce, diced green chilies, ground cumin, chili powder, salt, and black pepper. Simmer for 5 minutes, stirring occasionally.
Spread a thin layer of the beef mixture on the bottom of a 9×13 inch baking dish.
Place two tortillas over the beef mixture to cover the bottom layer.
Spread one-third of the remaining beef mixture over the tortillas.
Sprinkle one-third of the shredded cheddar cheese and Monterey Jack cheese over the beef layer.
Repeat layering two tortillas, one-third of the beef mixture, and one-third of the cheese two more times, ending with cheese on top.
Cover the casserole with aluminum foil and bake for 25 minutes.
Remove the foil and bake for an additional 10-15 minutes, or until the cheese is melted and bubbly.
Remove from the oven and let the casserole rest for 5 minutes before serving.
Sprinkle chopped fresh cilantro over the top before serving.