In a large pot or Dutch oven, combine the beans, onion, bell pepper, and garlic.
In a separate bowl, mix together the brown sugar, molasses, BBQ sauce, smoked paprika, mustard powder, salt, pepper, water, apple cider vinegar, and ketchup.
Pour the mixture over the beans and stir to combine.
Bring the pot to a simmer over medium-low heat and let it cook, stirring occasionally, for 30 minutes or until the sauce has thickened and the beans are tender.
For a smokier flavor, you can use handheld smoker or add a small amount of liquid smoke to the pot before simmering. You can also simmer on a smoker that has been brought up to temperature.
Enjoy your smoked BBQ beans as a side dish or use it as a topping for your BBQ ribs or pulled pork.