During the American Civil War, he was commissioned as a lieutenant colonel of the 18th Wisconsin Volunteer Infantry under Colonel James S. Alban. The 18th Wisconsin was organized in February 1862, proceeded to Tennessee in March, and was thrown into battle at Shiloh a day after their arrival. Beall was wounded in the battle and his leg was amputated below the knee. Colonel Alban was killed, along with the Regiment's third-in-command, Major Josiah W. Crane. After recovering, Beall served as second-in-command of a prisoner of war camp in Elmira, New York, where the prisoners nicknamed him "old peg-leg" and accused him of a pattern of repeated cruelty and abuse.