On 14 July 2003, during the ninth stage of the 2003 Tour de France, Beloki was in second place overall (just 40 seconds behind Lance Armstrong) and negotiating a turn at speed while descending the Cote de La Rochette, just 8 km from the stage finish at Gap. He lost control of his bicycle after his rear tire came off the wheel on a patch of tarmac that was softened by the sun (the road surface temperature was reported to be 50°C (125F), sending his rear wheel skidding first in one direction and then the other. Beloki suffered a hard fall that broke his right femur in two places, his elbow and his wrist. Armstrong was following immediately behind Beloki and, to avoid the fallen rider, headed off the road to go down the hill through the underbrush and across a small field. The crash effectively ended Beloki's career as a premier bicycle racer.
For the 2004 season, Beloki opted to sign for the French team Brioches La Boulangère in preparation for the 2004 Tour de France. He was reported as being fully recovered from his injuries by early 2004, but it later transpired that those injuries were taking longer to heal than initially anticipated. By mid-April 2004, Beloki had yet to begin serious competition for the season. He started his home race, the Vuelta al País Vasco, but failed to even complete the first stage before retiring in pain from his injuries. Citing incompatibility with the French team, he switched to the Spanish Saunier Duval-Prodir team for the remainder of the 2004 season. Beloki switched back to Manolo Saiz's team (now called Liberty Seguros-Würth) for 2005. Beloki completed the 2005 Tour de France and finished in 75th place.