2006 was Wilson's first full season in the WRC, as a driver for the Stobart VK M-Sport Ford team. He competed in all 16 rallies, and became the youngest ever world rally driver to win a stage (the Cordoba Stadium superspecial stage on Rally Argentina), and score championship points - when he finished eighth overall on that event. This record was later broken by Andreas Mikkelsen. He finished 28th in the season’s standings with one point, but was classified as a finisher in every event, an achievement no other driver managed in 2006.
It is well known in rallying that Malcolm Wilson has a five-year plan for Matthew, starting in 2006 and running right through until 2010. 2006 was intended as a 'learning' year, and Matthew was told to finish every rally, taking points as a bonus. In 2007, Jari-Matti Latvala and Henning Solberg were nominated for Stobart's manufacturer points, taking some pressure off Wilson and co-driver Orr. Wilson finished 11th in the driver's world championship with 11 points. His best result was fourth at the 2007 Rally Japan.
2008 began with an outing Wilson referred to as "moderate" - he finished 10th in Monte Carlo, scoring no points in drivers' nor manufacturers championship. It was his best result here so far; furthermore he had to adjust to new car, tyres and new-old co-driver, Scott Martin. In Sweden Wilson Jr. was aiming for a top-ten finish but even though his pace was good enough to achieve that, mechanical problems with the throttle forced him to retire from fifth place less than 30 km before the finish.. Wilson scored his first points of the season in México with a sixth place finish.
In September 2008, Wilson took part in the Colin McRae Forest Stages Rally, a round of the Scottish Rally Championship centred in Perth in Scotland. He was one of a number of WRC celebrity drivers to take part in the event in memory of McRae, who died in 2007. He went on to win the event comfortably in a 2005 spec Focus WRC.