After graduation from West Point in 1861, he enlisted in the Civil War on 07 February 1861 in Goshen, NY, joining the Union Army of Northeastern Virginia. He was less sensitive to his Southern heritage than his father, Major Alfred, Sr. He became a Jewish Civil War hero. He received high commendation for his conduct at the Battle of Bull Run by the order of the Department of War. Alfred served as chief ordnance officer in several Union regiments including Co. B, 8th N.Y. Cavalry. He received a promotion of Major on Sept 7, 1863 and he became a Lt. Colonel on March 13, 1865. In 1865, he was appointed instructor of ordnance and gunnery at the Military Academy. Colonel Mordecai became the Superintendent and Commandant of the Springfield Armory from 1892 to 1895. When he left the Army, he was promoted to Brigadier General.