When the American Civil War began in 1861 Jones volunteered for service in the Union Army. On October 3 he was elected captain of the 53rd Ohio Infantry Regiment, and saw action as such during the Battle of Shiloh and the Siege of Corinth. On May 2, 1862, Jones became colonel of the 53rd Ohio and its commanding officer. He led his regiment during the Siege of Vicksburg and at the battle of Missionary Ridge, both in 1863. Jones saw further action throughout the 1864 Atlanta Campaign, fighting at Resaca, Dallas, Kennesaw Mountain and Atlanta. In August, Jones was appointed to brigade command when his superior officer, Brigadier General Joseph A. J. Lightburn was wounded and relinquished command for the remainder of the war. Colonel Jones now led the 2nd Brigade in William B. Hazen's 2nd Division of the XV Corps at Jonesboro. Coincidentally, the 1st Brigade of that division was also led by another "Colonel Jones", Theodore Jones of the 30th Ohio. Wells Jones participated in the 1864 March to the Sea, and was wounded during operations around Fort McAllister, Georgia, on December 13.