Preheat the oven to 375°F (190°C). Lightly grease a 9×13 inch casserole dish.
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 soft, about 6-8 minutes. Drain excess fat if necessary.
Add the enchilada sauce, black beans, diced green chilies, ground cumin, chili powder, smoked paprika, salt, and black pepper to the skillet. Stir well to combine and cook for another 3-4 minutes until heated through.
Remove the skillet from heat. Stir in half of the shredded cheddar cheese and half of the Greek yogurt until evenly mixed.
In the prepared casserole dish, layer one-third of the tortilla quarters evenly on the bottom.
Spread one-third of the beef mixture evenly over the tortillas.
Repeat layering twice more with tortillas and beef mixture, ending with the beef mixture on top.
Sprinkle the remaining shredded cheddar cheese evenly over the top layer.
Cover the casserole dish with aluminum foil and bake for 20 minutes.
Remove the foil and bake uncovered for an additional 10-15 minutes until the cheese is melted and bubbly.
Remove the casserole from the oven and let it rest for 5 minutes.
Top with the remaining Greek yogurt and chopped fresh cilantro before serving.