Ganz moved to local rivals A.C. Milan in December 1997, helping the club to the 1998 Coppa Italia final during his first season with the club. In his second season, he won the Scudetto with Milan and was very influential, scoring several important goals, including one against his former team Inter in a memorable 5–0 win in a Milan Derby cup tie. His third season was less successful, as Milan were defeated by Parma in the 1999 Supercoppa Italiana final. Ganz did not find much space in the squad that season, and spent a lot of his time on the bench, as Alberto Zaccheroni, the Milan manager at that time, had several other star offensive players, such as Oliver Bierhoff, George Weah, Andriy Shevchenko, Leonardo, and Zvonimir Boban.