On 12 September 2006, Pizarro scored his first competitive goal for Roma in a 4–0 UEFA Champions League victory over Shakhtar Donetsk in the 89th minute. Five days later, he scored twice in a 3–1 Serie A win over Siena. He also helped Roma win the 2006–07 Coppa Italia title, where was one of the team top-scorers with three goals. On 20 June 2007, Roma announced they paid Inter the remaining 50% of Pizarro's rights to keep him at the club until 2010. The next season, he was an undisputed starter with Daniele De Rossi in midfield, making over 30 league appearances as well as in the UEFA Champions League, where he scored a goal in a 2–1 win over Real Madrid to seal the club's progression to the quarter-finals. Pizarro also won the Coppa Italia with Roma that season.