Preheat the oven to 375°F (190°C). Lightly grease a 9×13-inch baking dish.
Heat the olive oil in a large skillet over medium heat. Add the chopped onion and cook until softened, about 3-4 minutes.
Add the minced garlic and cook for 1 minute until fragrant.
Add the lean ground beef to the skillet. Cook, breaking it up with a spoon, until browned and cooked through, about 6-8 minutes. Drain any excess fat.
Stir in the black beans, enchilada sauce, diced green chilies, ground cumin, chili powder, smoked paprika, salt, and black pepper. Cook for 3-4 minutes, stirring occasionally, until heated through and well combined.
Spread a thin layer of the beef mixture on the bottom of the prepared baking dish.
Place one whole wheat tortilla over the beef layer. Spread about one-sixth of the beef mixture evenly over the tortilla. Sprinkle with about 1/3 cup of shredded cheddar cheese.
Repeat layering with the remaining tortillas, beef mixture, and cheese, ending with a layer of cheese on top.
Cover the baking dish with aluminum foil and bake for 20 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 enchilada bake rest for 5 minutes before serving.
Serve warm, topped with a dollop of Greek yogurt and a sprinkle of chopped fresh cilantro.