Preheat oven to 350°F.
In a large, ovenproof or cast-iron skillet, heat oil, 2 turns of the pan. Season the chicken on both sides with salt and pepper, and brown evenly; remove to a plate. Add onions and garlic, and stir 5 minutes to soften. Add spices and stir a minute to toast spices. Add tomatoes, chipotle, beans and slide chicken back into pan. Cover pan and bake 30 minutes, covered, then return to stove; remove chicken to plate. Simmer the sauce until ready to serve.