Dealing with the fallout from the academic scandals of the Haskins era, it was several years before Monson was able to recruit on equal footing with other Big Ten coaches. He led the Gophers to one NCAA Tournament and 4 NIT appearances in his 7 full seasons as Gophers coach. Nonetheless, he was widely praised for cleaning up the program's image. On November 30, 2006, Monson resigned as head coach of Minnesota after a 2–5 start and only achieving a single 20-win season in seven. Assistant coach Jim Molinari was appointed interim head coach before Tubby Smith was named the new head coach after the season. Monson compiled a 118–106 () record with the Gophers, giving him an overall career record of 170–123 () as a head coach.