Mix together the green beans, bacon, black pepper, jalapenos, onions and soup in a bowl until well blended. Transfer to two 9- by 13-inch metal baking dishes. Place in the smoker or bake until the onions are tender, about 1 hour 30 minutes.
Sprinkle the cheese over evenly, and cover the pans with aluminum foil. Let stand until the cheese melts, about 5 minutes. Stir to mix in the cheese and serve immediately, scooping directly from the dish.