The Lokeren-born player and manager used to coach among others Genk and Anderlecht with whom he won three Belgian championships in a row from 1999 until 2001 (the first with Genk, the following two with Anderlecht), and was also voted Jupiler League Coach of the Year those years. At Anderlecht, his team played its best UEFA Champions League season since the appearance of a group stage by winning matches against Real Madrid, Manchester United, Lazio Roma, PSV Eindhoven, and Dynamo Kiev. He was the national team coach of Belgium from July 2002 but his contract, running to July 2006 was not renewed after the team failed to qualify for Euro 2004 and the 2006 World Cup. On 1 January 2006, Anthuenis took up the post of manager of KSC Lokeren. It was his third spell managing the club. On 28 February 2006, he resigned as Lokeren boss and retired from football on health grounds, having been admitted to hospital with cardiac-related chest pains the previous week.
On 21 February 2010 EXQI League club Lierse hired the former K.F.C. Germinal Beerschot coach to replace Herman Helleputte who has become the club's technical director.