In 1989, Coloni entered two cars for Roberto Moreno and French newcomer Pierre-Henri Raphanel. The FC188Bs were another update of the 1987 car, but were hard to handle and about 20 km/h slower than the rest of the grid. Nevertheless, both drivers were able to qualify for the Monaco Grand Prix. This was the only race participation of a Coloni in the first part of the season. In Canada, Coloni presented a new car (the Coloni C3) which was penned by former AGS engineer Christian Vanderpleyn. The C3 was a basically good design but the team's performance suffered from lack of testing, often struggling to find the right setup for the races. The team failed to qualify for most of the rest of the season — only in three cases, the debut of the Coloni C3, the 1989 Canadian Grand Prix, the 1989 British Grand Prix and at the Portuguese Grand Prix did Moreno qualify, in 26th, 23rd and 15th place respectively, after a developmental front wing was fitted for Estoril. Unfortunately for the team, he then collided with Eddie Cheever in the warm-up.

Archived 2007-09-26 at the Wayback Machine and had to use the spare car. He did not finish the race as the engine blew up after a handful of laps. As results failed to arrive, the team was cut back throughout the year. After Vanderpleyn had left the team in September, Enzo Coloni took over the engineer's job himself but this brought no improvement; neither did the new driver Enrico Bertaggia who replaced Raphanel for the last races. The team finished equal 18th and last with Zakspeed. The Portuguese Grand Prix proved to be the last qualification for a Coloni car.