[1] Subsequently, he managed Belgian giants Racing Genk between 2001 and 2004, winning the Manager of the Year award at the Belgian professional football awards in 2001–02.

In 2008, Vergoossen was appointed interim manager of PSV Eindhoven in January 2008, whom he led to winning the 2007–08 Eredivisie title.

After his successful tenure at PSV ended, Vergoossen moved on to work for his previous club Genk as an advisor on a part-time basis.

In January 2009, after his successor Huub Stevens resigned at PSV, Vergoosen was named as one of the top candidates for the managerial role, having successfully led the side to the Eredivisie title the previous season.

[2][3] On 10 August 2022, Vergoossen returned to Roda JC to advise supervisory directors in the field of football technical matters.