Preheat oven to 350 degrees F (175 degrees C). Grease a 2 1/2-quart baking dish.
Combine pork and beans, kidney beans, lima beans, onion, brown sugar, ketchup, and dry mustard together in a bowl; transfer to the prepared baking dish. Sprinkle bacon over bean mixture. Cover dish with aluminum foil.
Bake in the preheated oven for 30 minutes. Remove aluminum foil and continue baking until bubbling, about 30 minutes more.