The MP4/5 arrived for 1989 as naturally aspirated engines became mandatory for all teams following the banning of turbocharged units. Honda developed a new 3.5-litre V10, the RA109E, built around the lessons of two years of the RA168E turbo programme. The monocoque was again produced in carbon fibre with assistance from Hercules Aerospace, with interchangeable aerodynamic components. The car was loosely based on the MP4/4 architecture, initially using the Weismann Longitudinal Transmission from its predecessor before a new transverse gearbox was introduced at mid-season.
Ayrton Senna remained at McLaren for 1989 while Alain Prost continued for what would be his final season at the team. Their personal rivalry had reached its breaking point during 1988, and the tension pushed both drivers to extract maximum development from the car, keeping McLaren's pace well ahead of the opposition despite the more competitive field that the engine parity of naturally aspirated regulations was expected to produce.
The MP4/5 was immediately fast, taking fifteen pole positions — thirteen by Senna, equalling his 1988 record. At the Mexican Grand Prix, Senna's 34th career pole broke Jim Clark's longstanding record of 33, which had stood since 1968. McLaren won ten races across the season, six for Senna and four for Prost.
Ferrari, with Nigel Mansell and Gerhard Berger, presented the strongest challenge, fielding the fast but mechanically fragile Ferrari 640 with its new semi-automatic gearbox. Ferrari's reliability problems ceded ground to McLaren throughout the year. The new transverse gearbox debuted on Prost's car at Silverstone, where Prost won; Senna went off at Becketts while struggling with the gearbox in his car during the same race.
The Drivers' Championship was decided at the penultimate round in Japan. Senna and Prost ran together at the front until colliding at the chicane on lap 46; Prost's race ended immediately while Senna restarted, pitted for a new nose section, overtook Alessandro Nannini's Benetton, and crossed the line first. Senna was subsequently disqualified for receiving a push start and for cutting the chicane when rejoining, awarding Prost his third World Championship.
Senna finished the season with four fewer points-scoring finishes than Prost despite winning more races. Prost won the Drivers' title; McLaren-Honda won their fourth Constructors' Championship of the decade. 1989 was also Honda's fourth consecutive Constructors' title as an engine supplier.
Prost moved to Ferrari for 1990, taking designer Steve Nichols with him. Gerhard Berger joined Senna at McLaren. Neil Oatley and his team redesigned the front and rear wings for the MP4/5B variant, reprofiled the rear bodywork to accommodate larger radiators, and introduced new venturi tunnels on the rear floor. Honda refined the engine, designated RA100E, and Senna invested heavily in development work to improve reliability.
The MP4/5B won six races and secured another Constructors' Championship, though the Ferrari 641 proved more closely matched in races than in qualifying. McLaren's outright pace advantage was most visible at power circuits such as Hockenheim and Imola, where both cars frequently qualified on the front row. The championship again came down to the Japanese Grand Prix: Senna and Prost collided at the first corner of the first lap, Prost retired, and Senna's title was secured.
Gordon Murray, who had joined McLaren from Brabham in 1987 and whose influence shaped the MP4/4 and MP4/5 generations, retired from Formula One after the 1990 season to work on McLaren's road car project.
A test mule designated MP4/5C was created during 1990 to develop Honda's new V12 engine for the following two seasons, making its public debut at a Silverstone test session with Allan McNish behind the wheel.
The MP4/5 and MP4/5B together produced 16 wins, 27 pole positions, 12 fastest laps, and 36 podium finishes from 32 races. The 1989 MP4/5 remains as of 2025 the last McLaren to win both the Drivers' and Constructors' Championships in the same season, and to have both its drivers finish first and second in the Drivers' standings. The two-car programme bridged the turbo era and the naturally aspirated era, maintaining McLaren's position at the front of Formula One while the rest of the field adapted to the new engine rules.