Mertes got his first college head coach position as the 24th head football coach for the Kansas State Wildcats in Manhattan, Kansas, and he held that position for five seasons, from 1955 until 1959. His coaching record at Kansas State was 15 wins, 34 losses, and 1 ties. As of completion of the 2007 season, this ranks him tenth at Kansas State in terms of total wins and 19th at Kansas State in terms of winning percentage.