In 1990, Goethals was named coach of Olympique de Marseille and was entrusted with the task of leading the club to European Cup success. In his first season, the club narrowly missed out on European glory, losing on penalties in the European Cup Final to Red Star Belgrade. There was recognition for Goethals' coaching abilities, as he was voted 1991 European Coach of the Year. In 1993, Marseille again reached the European Cup final, where they defeated favourites A.C. Milan with a headed goal by Basile Boli. Having achieved his primary objective at Marseille, Goethals left the club.