Leake resigned his seat in the state senate and became a captain of Company G of the 20th Iowa Infantry. He was commissioned a Lieutenant Colonel when the regiment was organized at Camp Kirkwood in Clinton, Iowa. He led the regiment at Prairie Grove, Vicksburg, Yazoo City, and Port Hudson. On September 29, 1863, in an engagement called the Battle of Stirling's Plantation near Morganza, Louisiana Leake was injured and captured by the Confederates. He was held prisoner at Camp Ford near Tyler, Texas. He was the highest ranking Union officer in the camp and he looked after the needs of the other Union POWs.