Initially, Bowyer was kept out of the Leeds first team by Alf-Inge Håland and David Hopkin; he eventually replaced Hopkin in the 1998–99 season, and from then on was a first-team regular. He was a key player in David O'Leary's Leeds side that qualified for the Champions League in 1999–2000, and which reached the semi finals of the UEFA Cup in 2000 and the Champions League in 2001. In the Champions League run he scored crucial goals against A.C. Milan, Barcelona and Anderlecht. He was voted the Leeds player of the year by supporters in both 1998–99 and 2000–01.