Andersen moved on to Germany in July 1990, where he played for German Bundesliga club 1. FC Köln. He did not win anything in his time with Köln. Though the club reached the 1991 DFB-Pokal cup final, they were beaten by Werder Bremen in penalty shootout. Following his knee injury at the UEFA Euro 1992, Andersen spent 11 months in rehabilitation, before he returned for Köln in May 1993. He soon thereafter suffered another knee injury to his cruciate ligament, and was out until February 1994. Following continued injury problems, he finally became fit for the 1996–97 season where he played 28 of 34 games. After another injury, he ended his career in May 1998, 33 years old, and went on to become a sports agent in December that year.