FIA GT

In 2004 Maserati completed three MC12 GT1 race cars intended for the FIA GT GT1 class. The AF Corse factory-backed squad debuted the race at Imola, yet the FIA did not allow the MC12 to score points due to its debated homologation. Even with this setback, the team managed to take second and third places. At the next round at Oschersleben, the MC12 of Andrea Bertolini and Mika Salo won for the first time. At the final round of the year at Zhuhai, the FIA finally agreed to homologate the MC12s and allow them to score points towards the championship. With this, the MC12 again took victory, allowing it to score enough points to finish 7th in the teams championship.

In 2005 Maserati won the FIA GT Manufacturers Cup with 239 points: almost double the score of next team (Ferrari with 125 points). The two teams that entered MC12s into the FIA GT, Vitaphone Racing and JMB Racing, finished first and second respectively in the Team Cup, with Vitaphone winning by a considerable margin. Four of the MC12 drivers were in the running to win the FIA GT Drivers' Title at the Bahrain International Circuit at the start of the final race of 2005: Karl Wendlinger and Andrea Bertolini each on 71 points and Timo Scheider and Michael Bartels on 70. Gabriele Gardel of Ferrari was also on 70 points, however, and in the crucial race he placed ahead of the all of the Maseratis, driving an older Ferrari 550 Maranello. Gardel took the title leaving all of the Maserati drivers within four points of first place (Scheider and Wendlinger receiving four points for the race).
 
In 2006 the only team representing Maserati was Vitaphone Racing. On October 1, 2006 Vitaphone secured victory for the 2006 season despite their drivers placing 5th and 7th, with weight penalties of 85 kilograms and 105 kilograms respectively. Vitaphone gained enough points to be "out of reach" of their nearest rival, Aston Martin Racing BMS (who race the DBR9). According to Vitaphone Sporting Director Rafael Calafell, the goal of Vitaphone Racing is now to win the Drivers' title.
 
Italian GT

MC12s have had great success racing in Italy, and have replaced the GT3 "Maserati Trofeo Light" as Maserati's representative in the Italian GT series. In 2005 Maserati introduced two MC12s to the GT1 division under Scuderia Playteam and Racing Box, with the teams placing first and third overall respectively. The cars were re-entered in 2006, with Scuderia Playteam again securing overall victory and Racing Box coming second. From 2007, GT1 cars are not permitted in the championship, and Scuderia Playteam moved to the FIA GT Championship.

Super GT

In 2006, the Le Mans winning outfit Team Goh was intending to race a Maserati MC12 in the Super GT series in Japan. However, the team was forced to withdraw because of driver problems (Jan Magnussen falling ill suddenly and returning to Denmark) and disappointing lap times at the Suzuka Circuit during testing. While the car was faster than its Super GT rivals down the straights, it was losing more than a second per lap in the corners due to its poorer aerodynamics.

American Le Mans Series

In 2004 the Maserati MC12s were unable to compete in series backed by the ACO, such as the Le Mans Endurance Series (LMES) in Europe and the American Le Mans Series (ALMS) because they exceeded both the length and width restrictions for their class. The car's nose was shortened by 200 millimetres (7.9 in) to attempt to comply with regulations, but was still 66 millimetres (2.6 in) too wide. In 2005 the governing body of the ALMS, the International Motor Sports Association (IMSA), allowed the MC12s to compete as a guest with the agreement that they were not allowed to score championship points and were forced to run a weight penalty. Some ALMS teams initially objected to the participation of the MC12 due to the possibility that an accident could eliminate their chances at the 24 Hours of Le Mans, but the MC12 was finally allowed to race. However the ACO stood by their ruling on the car by forbidding it from entering Le Mans.

The 2005 American Le Mans Series season was not as successful for Maserati as the previous FIA GT season, with the team scoring no wins. In the final race at Laguna Seca, the MC12 was clipped by a competitor, causing damage that resulted in a lengthy pit stop. After resuming the race, a loss of traction caused by cold tyres made the car hit a kerb, which broke the radiator and took the MC12 out of the race