In the 2007 Tour de France, he did not win a stage, partly because Rabobank was defending Michael Rasmussen's lead for a large part of the race. But he won three stages in the Vuelta a España. In the 2008 Tour, Freire wore the green jersey from stage 8. He won stage 14 and the points classification. In the 2009 Tour he and Julian Dean were shot by an air rifle during the 13th stage from Vittel to Colmar. He was shot in the thigh and finished the stage 117th.