When the Civil War began in 1861, Dye was a captain in the U.S. Army. However he accepted a commission as colonel of the 20th Iowa Infantry Regiment on August 25, 1862. In 1862 Colonel Dye commanded the 2nd Brigade, 2nd Division of the Army of the Frontier. Dye led the brigade at the battle of Prairie Grove where his division was under the overall command of Brig. Gen. Francis J. Herron. The following year, Dye returned to command of his regiment and was part of Herron's division of reinforcements sent to aid the Union army besieging Vicksburg.