He started the 2009–10 season with a goal against Sporting Clube de Portugal in a 1–1 return leg draw at Stadio Artemio Franchi, which gave Fiorentina their entrance into the Champions League group stages. Other decisive goals included goals against Palermo, Sampdoria, and Livorno. On 29 September 2009, he scored both goals in a 2–0 victory over Liverpool in the Champions League group stage. On 9 March 2010, Jovetić scored two goals in Fiorentina's 3–2 win over Bayern Munich. The club lost, however, on away goals, and he also scored again against Napoli on 13 March. He scored in a 4–1 win against Udinese on 28 March.