Caruso was accused in the Operación Puerto doping case, but his case was soon dropped by the Spanish federation. The Italian Olympic Committee wanted him suspended for two years, but he was acquitted of involvement by the Court for Arbitration for Sport. In 2009 he signed a contract until the end of 2011 for LPR Brakes–Farnese Vini, but moved to Ceramica Flaminia–Bossini Docce midseason. He had a contract with them through 2011, but on 6 April 2010, after the Giro d'Italia organizers had announced that Ceramica Flaminia was not invited to the race, he was allowed to break his contract and to sign with Team Katusha, who assumed the contract through its duration. The Team Katusha signed him mainly in order to put him at the head of the team in the Giro d'Italia 2010.In late 2011 he prolonged his contract for the upcoming season.
In August 2015, it was announced that Caruso had returned a positive test for EPO in March, 2012.