Bowden was previously the head coach at Salem University (1983–1985), Samford University (1987–1992), Auburn University (1993–1998), and the University of North Alabama (2009–2011) before becoming the head coach of the University of Akron. Bowden is the son of former Florida State University head football coach Bobby Bowden. 

In 1992, when he became the head football coach of Auburn, he became the first coach to go undefeated in his debut season at Division I school. That year he won the Eddie Robinson Coach of the Year award, the George Munger award, the Paul "Bear" Bryant Award, the Sporting News College Football Coach of the Year, the Walter Camp Coach of the Year, and the SEC Coach of the Year.