Preheat oven to 375 F.
Line a baking sheet with foil and add the bacon.
Bake for 30-40 minutes until crisp, turning once. Remove to a paper towel-lined plate to drain.
Cut peppers in half vertically. Remove any seeds.
Place peppers on a baking dish and fill the halves with the beer. Cover with foil and place in the oven for 20-30 minutes or until tender.
Meanwhile, crumble the bacon into a bowl and add the onion and cheeses.
Uncover the peppers and pour off any remaining beer. Fill cavities with the bacon mixture and return to the oven, uncovered, until the cheese is melted.