Combine cumin, paprika, oregano, and chipotle powder in a small bowl.
Heat oil in a large skillet over medium-high heat.
Add onion, garlic, and jalapeño; cook 3-4 minutes until softened.
Add ground beef and spice mix; cook 6-8 minutes until browned, breaking up meat as it cooks.
Drain excess fat, leaving a little for flavor.
Stir in refried beans, black beans, and 1/4 cup enchilada sauce until combined.
Season with salt and pepper, then remove from heat.
Preheat oven to 350F.
Spread 1/4 cup enchilada sauce in bottom of 9x13 baking dish.
Place 1/3 cup filling on lower third of each tortilla and sprinkle with cheese.
Roll tortillas tightly and place seam-side down in dish.
Pour remaining enchilada sauce over rolled enchiladas.
Sprinkle remaining cheese evenly over top.
Bake 15-20 minutes until cheese is melted and enchiladas are heated through.
Let rest 5 minutes before serving.
Serve with cilantro, sour cream, avocado, and extra jalapeños.