In a large skillet, cook bacon over medium heat until crisp. Remove with a slotted spoon to paper towels. Drain, reserving 2 tablespoons drippings. Saute onion in drippings until tender. In a very large bowl, combine the beans, pineapple, bacon and onion. Combine brown sugar and ketchup; stir into the bean mixture.
Transfer to two greased 3-qt. or 13-in. x 9-in. x 2-in. baking dishes. Cover and bake at 350° for 20 minutes. Uncover; bake 25-35 minutes longer or until bubbly and beans reach desired thickeness.