Under new manager Roberto Donadoni, Perrotta scored his second goal for Italy in a 3–1 away win over Georgia in a Euro 2008 qualifying match on 11 October 2006. He made his first appearance as Italy captain on 21 November 2007, in the second half of a 3–1 home win over the Faroe Islands, in a European qualifier. He went on to take part at UEFA Euro 2008, often appearing as an attacking midfielder, where Italy lost out to eventual champions Spain on penalties in the quarter-finals.