At Colorado, Barnett was suspended briefly in the 2004 offseason due to events stemming from allegations of sexual misconduct by several members of the football team.

The following year, the Wildcats won a share of the Big Ten title and reached the Florida Citrus Bowl, losing 48–28 to Tennessee.

Barnett turned a program holding the record for the longest losing streak in Division I-A into a championship caliber organization.

On September 26, 2015, Barnett was recognized with other recent Hall of Fame inductees during the half-time program at the Northwestern football team's home game against Ball State University.

In a 2017 article by the Chicago Tribune, it was noted that Barnett turned down head coaching jobs with Georgia and UCLA following the 1995 season.

During the 2004 season, his reputation took a hit due to a recruiting scandal, insensitive off-field remarks, and failure to maintain the on-field success of his predecessors.

That scandal, coupled with Barnett's dismissive comments about former placekicker Katie Hnida, who alleged that she had been raped by a teammate, led to a infractions from the University.

However, the Buffs lost to Iowa State, then suffered a 30–3 thrashing at the hands of Nebraska and a 70–3 blowout by the eventual national champion Texas Longhorns in the Big 12 championship game.

Additionally, an anonymous tipster wrote a letter to CU system president Hank Brown accusing Barnett of numerous improprieties, including tampering with sworn testimony.

In June 2007, the Buffaloes were placed under probation for two years and fined US$100,000 for undercharging 133 student-athletes for meals over a six-year span (2000–01 to 2005–06 encompassing Barnett's tenure at Colorado) resulting in the major infraction.

In September 2016, Barnett joined Denver AM radio station 850 KOA, as color commentator for Colorado Buffaloes Football Games, alongside play-by-play man, Mark Johnson.