Müller stepped up to International Formula 3000 for 1998 driving as a BMW Junior for the Oreca team, but only finished in 20th position. He opted to race in the French Formula Three Championship in 1999, and finished seventh. He then returned to the German championship in 2000, and finished as runner-up to Giorgio Pantano, driving for Team Ghinzani. In 2001, he raced for the team in Euro 3000, and finished third in the standings behind Felipe Massa and Thomas Biagi. Müller returned to International F3000 in 2002, driving the first five rounds for Durango before moving to European Minardi for the next four rounds, but he failed to score any points during his nine races and separated from the team with three rounds remaining.
Müller returned to Formula Three in 2005, racing for his old team Ghinzani in the Italian Formula Three Championship. He finished as runner-up to Luigi Ferrara, nine points behind, having had twenty points taken away for a technical irregularity.
After sitting out the 2006 season, Müller once again raced in the Spa 24 Hours, this time for Scuderia Playteam Sarafree, finishing 18th in a Maserati MC12.
For 2008, Müller raced full-time in the FIA GT Championship for Jetalliance Racing in their second Aston Martin DBR9, alongside owner Lukas Lichtner-Hoyer. Müller set pole position for the second race of the season at Monza, but the car did not finish the race. The car did finish second at Oschersleben behind its sister car driven by Ryan Sharp and Karl Wendlinger.
Müller was signed by the Vitaphone Racing Team for the 2009 season, to race its second Maserati MC12, as teammate to Miguel Ramos. The pair finished eighth in the standings, after scoring three pole positions. They helped Vitaphone to win the teams championship. Müller also finished third in the GT1 class at the 24 Hours of Le Mans with Jetalliance, having set class pole position.