Heat beer and butter together in a saucepan over low heat until butter is melted and temperature reaches 115 to 120 degrees F (45 to 50 degrees C).
Stir pepper jack cheese, Asiago cheese, onions, and jalapeno peppers together in a bowl.
Place beer and butter mixture into bread machine pan, add sugar, salt, and flour, respectively. Create a small well about 2-inches deep in the flour and add yeast; push flour over yeast to cover. Add about half the cheese mixture.
Select Basic or White Bread cycle and start machine.
After the cycle has been running for 30 minutes add remaining cheese mixture. Continue processing in bread machine. Remove loaf from machine and place on a wire rack until cool, about 20 minutes.