In 2006, Scarponi was implicated in the Operación Puerto doping case. Despite this, and Scarponi's cycling team folding, Scarponi was able to secure a contract with Acqua & Sapone.
Despite a promising start to the 2007 season, Scarponi was once again implicated in the Operación Puerto case. On May 8, 2007, Scarponi confessed his role in the case.
With the rider completing his ban, announced on June 13, 2008 that they had signed Scarponi for the coming two seasons. In 2010 he finished fourth overall in the Giro d'Italia, and in 2011 second overall behind Alberto Contador.