Preheat smoker to 250–275 °F (120–135 °C) using preferred wood such as hickory, apple, or mesquite.
Cook chopped bacon in a skillet over medium heat until partially crisp, then remove and set aside.
Sauté diced onion and optional jalapeño in bacon fat until softened.
Combine baked beans, cooked bacon, sautéed onion, BBQ sauce, brown sugar, molasses, mustard, Worcestershire sauce, smoked paprika, garlic powder, and black pepper in a large cast-iron skillet or foil pan. Stir well.
Place the pan uncovered in the smoker and smoke for 2 to 3 hours, stirring occasionally, until the beans are thick, bubbly, and deeply smoky.
Serve hot as a side dish with grilled or smoked meats.