He was previously the head men's basketball coach at Southern Illinois University Carbondale.

On March 1, 2007, Lowery was named Missouri Valley Conference Coach of the Year after leading SIU to a 25–5 regular season record.

A highlight win for the season was when they beat the highly ranked Butler Bulldogs on the road.

On March 10, 2011, Lowery received a vote of confidence from athletic director Mario Moccia at a joint press conference, despite Southern Illinois suffering its third season with a .500 record or below and growing pressure from fans and alumni to fire Lowery.

[2] Lowery and the Salukis continued their losing ways in the 2011–12 season, posting a career-low 8–23 overall record with a 5–13 mark in conference play.