- In 1992, Bowden was hired to succeed Pat Dye as the head football coach at Auburn University
- During his first year at Auburn, Bowden led the Tigers to a perfect 11–0 season, becoming the first coach to go undefeated in his debut season at a Division I school. In 1994, Auburn finished 9–1–1, establishing the longest winning streak in school history at 20 games.
- In 1997, Auburn reached the SEC Championship Game, where they held as much as a 20–7 lead, but lost, giving up a fourth quarter 73-yard touchdown pass by Peyton Manning of the Tennessee Volunteers.
- In 1998, Bowden’s fate at Auburn changed as he faced criticism for recruiting woes, off-the-field issues that resulted in player discipline, and in his relationships with Auburn administrators, including board of trustees member Bobby Lowder. These issues, combined with a string of player injuries, led to a disastrous start of the 1998 season.
- After starting 1998 with a 1–5 record, Bowden resigned as head coach the night before Auburn played against Louisiana Tech. In conversations with athletic director David Housel, Bowden was given no assurances he would have a chance to remedy the situation for the next season, and that he believed his termination was imminent. The team was coached for the remainder of the season by Bill Oliver.