Preheat oven to 250 degrees F (120 degrees C).
Place pork roast into a large baking dish and scatter sauerkraut around the roast. Arrange apple and onion quarters around the roast. Sprinkle sauerkraut, apples, and onions with brown sugar. Pour beer over roast and sauerkraut mixture. Cover dish with aluminum foil and seal foil to the edges of the dish.
Bake in the preheated oven until roast is tender and pan juices are reduced, 3 to 4 hours. If roast, vegetables, and apples seem dry, pour in 1 more can beer. To serve, gently toss sauerkraut with apple and onion quarters and serve with the roast.