In 2000, Vaughters joined the French team Crédit Agricole. In the early part of the season he was third in the Tour Méditerranéen, sixth in Paris-Nice and in the Critérium International. In June, he was fifth in the Critérium du Dauphiné Libéré, after placing fourth in the stage including Mont Ventoux. In July, he participated in the Tour de France and abandoned during the tenth stage after a fall on the descent of the Col de Marie-Blanque. In 2001, he won the time trial in the Dauphiné Libéré, and the Duo Normand with teammate Jens Voigt. During the Tour de France, he was part of the winning team in the team time trial. He was again forced to retire from the Tour, however, suffering from a wasp sting above his right eye during the 14th stage (the UCI prohibited the use of cortisone injected intramuscularly or intravenously for the treatment of wounds, although it could be directly injected, e.g. for tendonitis). In 2002, he participated in his fourth and final Tour de France as a rider but failed again to reach the end of the race. He abandoned at the eleventh stage after falling in the descent of the Col d'Aubisque. Following the abandonment, he requested and received the termination of his contract with Crédit Agricole which had been due to run until the end of 2003. He retired from racing, citing a desire to spend more time with his family.