Preheat the oven to 400 degrees F. Line a rimmed baking sheet with aluminum foil.
In a large skillet, cook the onions and bacon over medium heat until crisp. Remove the mixture from the skillet and set aside. In the same skillet, add the bourbon and cream cheese and stir constantly until the cream cheese is melted and mixed with the bourbon. Add the onion and bacon mixture back into the skillet and mix together. Add the breadcrumbs, salt and pepper and mix together.
Spoon the mixture into the mushroom caps and place on the prepared baking sheet. Bake until the mushrooms are tender, 25 to 35 minutes. Top with some Parmesan and put back into the oven to allow the cheese to melt. Remove from the oven and serve.