As the American Civil War broke out, Governor Samuel J. Kirkwood granted Benton the military rank of colonel and tasked him with organizing the 29th Iowa Infantry Regiment.

Following the Battle of Bayou Fourche, the 29th Iowa, under Benton's command, protected the home of Confederate general Albert Pike.

Benton was elevated to the rank of brevet brigadier-general and returned to Iowa after the war ended.

Benton contested the 1865 Iowa gubernatorial election as a Democratic candidate opposed to African-American suffrage, and lost to Republican incumbent William M. Stone.

After Andrew Johnson assumed the presidency following the assassination of Abraham Lincoln, the Republican Assessor of Internal Revenue was removed from office, and Benton took on the position.