The 456M (M standing for Modificata) was unveiled in 1998, starting with chassis number 109589. Many changes were made to improve aerodynamics and cooling and the interior – still featuring Connolly Leather – was refreshed with new seats and other conveniences (fewer gauges on dash, and a new Becker stereo fitted in front of the shifter rather than behind as in the very shallow and special Sony head unit in the 456 GT). The 456 had a smaller grille with fog lights outside the grille. The undercarriage spoiler on the 456M is fixed, where the older 456 had a motorised spoiler that began its deployment above 105 km/h (65 mph). The hood was the first commercial application of carbon fibre, the previous being made of a composite material. Power output remained unchanged on the Modificata using Bosch Motronic M5.2 engine management at 442 PS (325 kW; 436 hp); the cylinder firing order was changed for smoother running and the torque remained the same for later versions of the 456 GT.

In the final year of production 2002/3, customers could specify their vehicle using the Carrozzeria Scaglietti Program. Launched at the 2002 Geneva Motor Show using Michael Schumacher’s own 456M GT as an example, customers could work with Ferrari personnel to create a highly individual car. Schumacher’s car had a two colour paint scheme, custom leather interior, re-worked instruments, an uprated handling pack and cross-drilled Brembo brakes. Such cars would be thus designated as a Tipo 456M GT(A) Scaglietti. The car is also calls the 456M GT “Schumacher Edition” as Schumacher was the first to commission the car. A total of 30 cars were produced, with only 10 being made with the 6-speed manual transmission.