At the beginning of the Civil War, Jones enlisted and served in the Eighth Texas Cavalry regiment (better known as “Terry’s Texas Rangers”) under the command of Benjamin Franklin Terry. He was later promoted to the rank of major. Jones was an active Mason, and in 1879 he achieved the position of Grand Master of the Grand Lodge of Austin. He died in Austin on July 19, 1881, while still in command of the Frontier Battalion, which continued to be operational until 1901.