Years of drought followed as Julich and Vandenbroucke left the team. Vandenbroucke's Belgian compatriots, Nico Mattan, Chris Peers, Peter Farazijn, and Jo Planckaert, stayed on but were criticised for inconsistent performances. Cofidis, on the demand of Migraine, began paying riders by results, judged by the points they won in a season-long competition run by the Union Cycliste Internationale. Belgian riders criticised the policy, saying it would lead riders to ride conservatively to be sure of good placings at the finish. They debated the issue publicly with the manager, Alain Bondue, and left.
David Millar raised the team's profile by winning the prologue of the 2000 Tour de France, taking leadership of the team. Millar criticized the points system and the team relented.
In 2004 Cofidis had three world champions – Igor Astarloa on the road, David Millar in the individual time trial and Laurent Gané on the track. However, a doping scandal involving Millar and other riders led them to stop racing until it was resolved. Astarloa left the team. The investigation decided that doping was by individual riders and that the team was not involved. David Millar has since suggested otherwise, in a strongly worded interview with the BBC.[2] In May 2004 the team announced that Bondue and team doctor Jean-Jacques Menuet had both resigned.[3] The team then returned to competition for the 2004 Tour de France, in which Stuart O'Grady and David Moncoutié won stages, Moncoutié's on Bastille Day.
Following the doping scandals, the team appointed Éric Boyer as team manager in 2005.[4] Moncoutié won on Bastille day again in the 2005 Tour de France – the only French stage win – with O'Grady's help. A new signing, Sylvain Chavanel failed to win a stage or to make a strong impression.
On 25 July 2007 Cofidis rider Cristian Moreni failed his doping test after the 11th stage of the Tour de France. His blood contained traces of testosterone. Moreni acknowledged doping. The team withdrew from the Tour.[5]
On 29 September 2009, the UCI ProTour decided not to renew the ProTour licenses of Cofidis and Bbox Bouygues Telecom, due to poor results.
[6]
In 2012, the team received a wildcard invitation to the Tour de France, along with three other French-registered teams.[7] A few days before the start of the race, Boyer was sacked as manager of the team, with Migraine blaming him for poor results: he was replaced by former Festina, Astana and FDJ–BigMatdirecteur sportifYvon Sanquer.[4][8]
On 10 July 2012, the first rest day in the 2012 Tour de France, French police raided the Cofidis team hotel, arresting French rider Rémy Di Gregorio[9] on suspicion of doping.[10]
After a 2017 season during which the team only took 13 wins, in October of that year the team announced that Sanquer had been sacked, and that he would be replaced as manager by former Cofidis rider Vasseur.[8]
The team returned to UCI WorldTour status in the 2020 season, and the team will using De Rosa bikes beginning from the 2020 season, ending their contract with Kuota.[12]
Starting with the 2023 season the team will be riding Look bicycles.[13]
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