Once the Civil War began, Matthies immediately volunteered for the Union Army. On May 14, 1861 he became a captain in the 1st Iowa Volunteer Infantry. Soon after on July 23, 1861 he was appointed lieutenant colonel of the 5th Iowa Volunteer Infantry. Matthies first saw action at the Battle of Island Number Ten. He was appointed colonel on May 23, 1862 and fought at the battles of Iuka and Corinth. During the winter of 1862-1863 he was in command of a brigade in the Army of the Tennessee.