In a large cast iron skillet, cook bacon pieces over a grill or stove until crispy. Drain on paper towels or newspaper. Set aside. Reserve 2 tablespoons of the bacon grease.
In the same pan, saute peppers and onions until they are tender and the onions are caramelized.
Pour the drained baked beans into the skillet, and add the bacon, bbq sauce, brown sugar, pickle relish, mustard and pepper. Stir well to combine.
Place pan in the smoker, and slow cook for several hours until excess liquid is evaporated, beans are bubbly and cooked through. The longer they are on the smoker, the stronger the smoked flavor will be. We smoked our beans for 2 hours on a smoker around 250 degrees.