After a period spent playing for Renaisiènne, he moved into coaching with Hannutois and Waremme, and led Sint-Truiden to second place in the Belgian First Division in 1966.

Belgium hosted the 1972 European Championship, having knocked out holders Italy in the qualifying stages, and defeated Hungary in the match for third place after losing in the semi-final to eventual tournament winners Germany.

Seemingly preoccupied with winning his first Belgian title, Goethals had suggested and initiated the bribing of the Waterschei players prior to the teams' meeting in the final match of the season, in order to secure championship honours for Standard Liège and ensure that none of his players would miss their European final against Barcelona through injury.

He then returned to Belgium to coach Racing Jet de Bruxelles before a second spell in charge of Anderlecht, where he won Belgian Cup trophy in 1989.

In 1990, Goethals was named coach of Olympique de Marseille and was entrusted with the task of leading the club to European Cup success.

Goethals' coaching career ended at Anderlecht in season 1995–96, but he remained in demand as a television analyst for his insights into football.

In 2005, the year following his death, he was voted 38th in De Grootste Belg, a Flemish television programme based on the BBC's 100 Greatest Britons.