Preheat the oven to 325 degrees F. Spray a 9-by-13-inch baking dish with cooking spray and set aside.
Place a large cast-iron skillet over medium heat until hot, then add the bacon and fry until almost crisp, 10 to 12 minutes. Remove to a paper towel-lined plate and set aside.
Add the onion and peppers to the same skillet to cook in the bacon grease until tender, about 5 minutes. Add the pork and beans, barbecue sauce, brown sugar, vinegar, jalepenos, mustard, salt and pepper, then stir to combine. Bring to a simmer, then transfer to the prepared baking dish. Cut the bacon into large pieces and place on top of the beans. Transfer to the oven to cook until bubbly and syrupy, about 2 hours.