At Weber State, he was best known for leading the Wildcats to an upset of North Carolina in the first round of the 1999 NCAA Tournament. To date, Abegglen is the only coach since the NCAA eliminated first-round byes in 1980 to defeat the Tar Heels in the first round. However, the circumstances of that triumph were overshadowed by the events surrounding it: Abegglen had been arrested for domestic violence against his then-wife earlier in the season. She had filed for divorce and Weber State forced Abegglen to resign whenever the team was defeated in the tournament.
Abegglen is the all time coaching winning percentage leader of the UAA Seawolves with a lifetime record of 109-45 for a .708 winning percentage. His tenure at UAA was highlighted by a 1989 win over the eventual national champion Michigan Wolverines 70-66 one of only two loses for the wolverines that year.