Cook the bacon. Add the chopped bacon to a skillet over medium heat and cook until the fat renders and the bacon starts to crisp.
Sauté the vegetables. Add the diced onion, bell pepper, and jalapeños to the skillet with the bacon. Cook for 4 to 6 minutes, stirring often, until the vegetables soften.
Drain the pineapple. Drain the crushed pineapple or pineapple chunks so the beans do not get watery.
Mix the beans. In a cast iron skillet, Dutch oven, or foil pan, combine the baked beans, cooked bacon and vegetables, drained pineapple, brown sugar, ketchup, and dry mustard.
Add optional flavor boosters. Stir in BBQ rub, Worcestershire sauce, apple cider vinegar, BBQ sauce, hot sauce, black pepper, smoked sausage, pulled pork, or brisket if using.
Preheat the smoker. Set the smoker to 275°F using apple, cherry, pecan, hickory, or oak wood.
Smoke the beans. Place the pan of beans on the smoker uncovered. Cook for 1 1/2 to 2 hours, stirring once or twice, until the beans are hot, bubbly, smoky, and thickened.
Rest the beans. Remove the beans from the smoker and let them rest for 10 minutes before serving.
Serve. Serve warm with ribs, pulled pork, burgers, hot dogs, smoked chicken, brisket, or your favorite backyard BBQ meal.