He was then promoted to brigadier general a month later on May 26, 1862, for his services at Shiloh. Moore then participated in the Second Battle of Corinth where he forced the Union troops to retreat over a mile away from their original position. Moore was then sent to reinforce the Confederate troops at Siege of Vicksburg and was then captured at Vicksburg's surrender. After a prisoner exchange Moore was put under the command of General Hardee with whom he fought during part of the Chattanooga Campaign. Disputes between Hardee and Moore led to Moore requesting a transfer from Jefferson Davis. The request was denied and John Moore resigned his commission as a brigadier general in the Confederate service in February 1864.