In 1862, he became a major general and commanded a corps in the Army of the Cumberland. He fought at the Battle of Stones River and the Battle of Chickamauga. He became commander of the Army of the Cumberland during the Chattanooga Campaign in 1863. He continued commanding the army during the Atlanta Campaign. When William T. Sherman started his March to the Sea, Thomas was left behind to defend Tennessee against John Bell Hood. Thomas defeated Hood at the Battle of Nashville in December 1864.