In 2016, he started his season with a win in the Dubai 24 Hour with Belgian Audi Club Team WRT. On 21 November 2016, Vanthoor quite literally flew and won the FIA GT World Cup, crowning himself as World Champion on the streets of Macau. On 3 December 2016, it was announced that Vanthoor would change from Audi to Porsche and the focus would be on the WeatherTech SportsCar Championship where he will drive a Porsche 911 RSR together with Kevin Estre. During his last race with Audi, he won the Sepang 12 Hours together with Robin Frijns, Christopher Haase and Phoenix Racing. With this he crowned himself as the first winner of the Intercontinental GT Challenge.