He served as an infantry officer in the Union Army in the Western Theater during the American Civil War, and was breveted a brigadier general near the end of the conflict.

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.

Colonel Jones now led the 2nd Brigade in William B. Hazen's 2nd Division of the XV Corps at Jonesboro.

Wells Jones participated in the 1864 March to the Sea, and was wounded during operations around Fort McAllister, Georgia, on December 13.

[2] On March 13, 1865, Jones was breveted a brigadier general, cited for "gallant and meritorious services" during the war.