The 3-month enlistment ran out, but the regiment was re-mustered, and on 31 August 1861, McGinnis was again made lieutenant colonel with Wallace as colonel. Due to the style of training, the regiment became known as "Wallace's Zouaves". On 3 September, Wallace was promoted to brigadier general and McGinnis became colonel of the regiment. McGinnis led the regiment during the capture of Fort Henry and then overland toward Fort Donelson. During the Battle of Fort Donelson, his regiment was temporarily attached to Lew Wallace's division and fought in the counterattack on the Union right. He received the praise of Lew Wallace for his actions that battle. McGinnis also led his regiment in the following battles of Shiloh and Corinth.