Clayton's regiment fought at the Battle of Stones River in the early winter as a part of the brigade of Brig. Gen. Zachariah Deas. Clayton suffered a severe wound, but recovered and was promoted to brigadier general in April 1863. He was assigned command of a brigade previously led by Alexander P. Stewart consisting of the 18th, 32nd, 36th, 38th, and 58th Alabama regiments. Clayton was active in a number of subsequent campaigns and battles, including Chickamauga and Chattanooga. His brigade played a prominent role in several fights during the 1864 Atlanta Campaign. Following the Battle of New Hope Church, Clayton was promoted to major general and assigned command of Stewart's division in the Army of Tennessee, where it participated in the unsuccessful Franklin-Nashville Campaign.