Preheat the oven to 375°F (190°C). Lightly grease a 9×13 inch baking dish.
In a medium skillet, heat the olive oil over medium heat. Add the chopped onion and cook for 3-4 minutes until softened.
Add the minced garlic, ground cumin, chili powder, smoked paprika, salt, and black pepper to the skillet. Cook for 1 minute until fragrant.
In a large mixing bowl, combine the shredded chicken, black beans, cooked onion and spice mixture, and chopped cilantro. Mix well.
Pour 1/2 cup of the enchilada sauce into the bottom of the prepared baking dish and spread evenly.
Warm the whole wheat tortillas slightly to make them pliable, either in the microwave or on a skillet for 10 seconds each side.
Place about 1/3 cup of the chicken mixture into the center of each tortilla. Sprinkle about 2 tablespoons of shredded cheddar and Monterey Jack cheese on top of the filling.
Roll up each tortilla tightly and place seam side down in the baking dish.
Pour the remaining enchilada sauce evenly over the rolled tortillas.
Sprinkle the remaining shredded cheese evenly on top of the enchiladas.
Cover the baking dish with aluminum foil and bake for 20 minutes.
Remove the foil and bake for an additional 10 minutes until the cheese is bubbly and slightly golden.
Remove from the oven and let cool for 5 minutes before serving.
Serve enchiladas topped with a dollop of low-fat Greek yogurt and extra chopped cilantro if desired.