During the American Civil War, Morgan engaged in manufacturing munitions for the Confederates until Nashville's occupation by Union forces. He was also a Confederate official, serving as chairman of the Central Bureau of Military Supplies in Nashville during the War. Morgan had two sons killed during the war serving in the Confederate States Army. His nephew, Brig. Gen. John Hunt Morgan of Alabama, served with the Confederate cavalry and gained fame as the leader of Morgan's Raiders. He was killed in 1864.