Fry bacon in a large cast iron skillet over medium heat for about 3 minutes. Don't cook the bacon until it's crispy because it will finish cooking in the smoker. Remove and set aside. This can be done on the stovetop or smoker.
In the same skillet using the bacon dripping, sauté the onion, jalapeno, bell pepper, and garlic until soft and translucent.
Add the kidney and pinto beans to the skillet, along with the apple cider vinegar, ketchup, mustard, brown sugar, Worcestershire sauce, molasses, barbecue sauce, Cajun seasoning, and pepper. Stir everything until well combined.
Place the partially cooked bacon on top of the beans.
Place the skillet in the pellet grill or on a charcoal grill and smoke for 2-3 hours or until the beans' flavors have melded together. Check the liquid level: If the beans start drying out, add more barbecue sauce or water to keep them moist.
Serve hot, and enjoy your delicious smoked baked beans!