Koller's career as coach started at the Swiss club FC Wil in the season 1997/98. In January 1999 he went to FC St. Gallen in the Swiss Super League. The next year the club won the championship for almost 100 years. In the UEFA Cup the Swiss team could eliminate English top club FC Chelsea. Koller was voted Swiss manager of the year 2000. From 2002 till 2003 he managed his former club Grasshoppers Zürich. His first club abroad was in the German Bundesliga where he managed 1. FC Köln. Being not successful he resigned after seven months. At this time Lukas Podolski made his first match in the Bundesliga.