Moore served as aide-de-camp to General Joseph E. Johnston between October 1861 and May 31, 1862 and, after Johnston was wounded at the Battle of Seven Pines, as aide-de-camp to Lieutenant General James Longstreet between May 31, 1861 and July 1862. Moore's regiment had been in Longstreet's brigade during the First Bull Run Campaign. In December 1862, Moore was appointed judge advocate general for the Confederate Trans-Allegheny Department and began two years of court martial duty. On April 28, 1863, he was appointed colonel, CSA, and judge advocate general. In January 1864, he became judge advocate general for the Department of Richmond. From May 18, 1864 to December 1864, he was a brigade commander of the Reserve Forces of Virginia, which he helped organize under the direction of Brigadier General James L. Kemper. On September 20, 1864, Moore was promoted to brigadier general. Between December 1864 and April 1865, he was in command of Brigade 1 of the Virginia Reserve Forces (local defense troops) in the Department of Richmond.