Soak the beans in water (the water should rise a few inches above the beans) overnight.
Cook the bacon on the sauté setting of the slow cooker, or in a Dutch oven on the stovetop. Remove the bacon and set it aside.
Drain all but 2 tablespoons of the bacon grease. Sauté the onion, pepper, and garlic in the grease until soft, about 5-7 minutes. If you cooked them in a Dutch oven, transfer the vegetables to the slow cooker.
Drain the beans. Add the beans and 3 cups of fresh water to the slow cooker. Cook on high for 3-4 hours, or until the beans are mostly tender.
Whisk the brown sugar, barbecue sauce, vinegar, mustard, and molasses together in a small bowl. Stir into the beans. Add the bacon to the slow cooker.
Cook an additional 1-2 hours on high, until the beans are thick and dark.
Notes
To make this recipe gluten-free, use a homemade gluten-free barbecue sauce, or be sure to check the labels of commercial barbecue sauces—some are gluten-free, but many are not!