In Grant's Vicksburg Campaign, Logan commanded the 3rd Division of James B. McPherson's XVII Corps, which was the first to enter the city of Vicksburg in July 1863 after its capture. Logan then served as the city's military governor. In November 1863 he succeeded William Tecumseh Sherman in command of the XV Corps; and at the Battle of Atlanta (July 22, 1864), after the death of James B. McPherson during the day, he assumed command of the Army of the Tennessee. He was relieved a short time afterward by Oliver O. Howard. He returned to Illinois for the 1864 elections but rejoined the army afterward and commanded his XV corps in Sherman's Carolinas Campaign.