Bowden led the Zips to a 5–7, 3–5 record in MAC play to finish in a tie for third place in the MAC East Division in 2016. The season began with a victory over VMI. The next week, Akron went to Madison, Wisconsin for a showdown against No. 10 Wisconsin. The Zips lost the game by a score of 54–10. Next, the Zips defeated Marshall by a score of 65–38, the most points Marshall had allowed in a football game in 25 years. The next week, Akron lost to Appalachian State before defeating Kent State and Miami (OH). After getting blanked 41–0 by No. 24 Western Michigan, the Akron Zips beat Ball State by a score of 35–25. The Zips would then lose its last four games of the season, beginning with Buffalo, then Toledo, Bowling Green and Ohio.