Before resigning his seat, Union Army Colonel Logan served in the army of Ulysses S. Grant in the Western Theater and was present at the Battle of Belmont on November 7, 1861, where his horse was killed, and at Fort Donelson, where he was wounded on February 15, 1862. Soon after the victory at Donelson, he resigned his seat on April 2, 1862 and was promoted to brigadier general in the volunteers, as of March 21, 1862. Major John Hotaling served as his chief of staff. To confuse matters, the 32nd Illinois was commanded at Shiloh by a different Colonel John Logan. During the Siege of Corinth, John A. Logan commanded first a brigade and then the 1st Division of the Army of the Tennessee. In the spring of 1863, he was promoted to major general to rank from November 29, 1862.