The 2016 season saw Flowers increase all his passing stats from the prior year. Entering the bowl game, Flowers eclipsed his post-bowl game numbers from 2015 in yards, completions, completion percentage and average per game while lowering his interceptions.
- Flowers finished the regular season completing 184-299 (61.5%) passing attempts for 2,551 yards and a season record tying 22 touchdowns.
- Against NIU, Flowers set a career high with 350 passing yards while matching his career high of four touchdown passes in the process.
- In the win at Memphis, Flowers set a school record for single game completion percentage at 82.7% (24-29).
- The team's leading rusher, Flowers totaled 1,425 yards on the ground on 177 attempts, an average of 8.03 yards per carry, which ranks third in the country.
- Flowers' average of 118.8 rushing ypg ranks 15th nationally and second among quarterbacks.
- His 15 rushing touchdowns are tied with Marlon Mack for the team lead, which is a season record.
- Flowers has eclipsed the century mark in rushing seven times on the season, including the last four regular season games.
- Flowers led the team in rushing in six games this season. His 210-yard performance against Memphis was a team season-high and a new American Conference record.