Early into his debut season, Stojković sustained a knee injury for which he had to have surgery in Germany, forcing him to the sidelines for months. In fact, the entire 1990–91 league season was injury riddled for the Serb and he ended up making only eleven league appearances. Beckenbauer stepped down from the coaching post during the winter break, although he remained with the club in an adviser capacity. The new head coach to replace the famous German was Raymond Goethals. In the final of the UEFA European Champions' Cup, Marseille played against Stojković's former team Red Star. Stojković, a penalty kick specialist, entered the game late during the extra-time as a substitute, but as the match eventually went to a penalty shootout, he informed head coach Goethals that he did not want to take a penalty shot against his former team. Red Star won the European Cup in the shootout.