Starting in the 2009–10 season, Miccoli took the role of captain leading the team through the campaign in place of the injured Fabio Liverani, and being then confirmed after the latter rejoined the team in November 2009. During the 2009–10 season, Miccoli scored 19 goals, tying him for third in the Serie A goal-scoring race. He scored a hat-trick on 27 March 2010 against Bologna, and in a home draw against Sampdoria on 9 May 2010, Miccoli scored his 41st goal in Serie A for Palermo on a penalty which he had earned, making him the all-time Serie A leading goalscorer for Palermo. The Luciano Zauri foul that earned Miccoli the penalty against Sampdoria, though it resulted in a successfully converted penalty, also caused a moderate injury to Miccoli's knee. As a result, Miccoli underwent right knee surgery on 13 May 2010 at the Villa Stuart Clinic in Rome. The moderate damage to his cruciate ligament was deemed "successfully repaired" by knee specialist Professor Pier Paolo Mariani, and Miccoli was expected to make a full recovery over the summer months.