 Kovačević once again reached top form for the Piraeus based club, scoring 17 goals in the Greek Superleague to lead Olympiacos to the league championship, and adding 3 goals in the Champions League as the team reached as far as the Round of 16.Kovačević scored twice in the UEFA Cup 1st round 5–0 home leg win against FC Nordsjælland.In early 2009, he was diagnosed with a blocked artery; he successfully underwent heart surgery to improve the flow of blood to his heart.