Jones, often called "Jenk", enlisted in 1862 in the 6th Battery of the Wisconsin Volunteer Army. His military service included the battles of Vicksburg, Missionary Ridge, Chattanooga, Lookout Mountain and Atlanta. He suffered a broken foot at Missionary Ridge that required him to walk with a cane for the rest of his life. His experiences during the war convinced him that people must find another way to settle their differences. After he was mustered out of the army, Jones became an outspoken pacifist.