 During the 2008–09 season, he was again Köln's top goalscorer with 16 Bundesliga goals to his name.On 12 September 2008, coach Christoph Daum made him captain of the first team squad, however in late November 2009, he lost his captaincy due to a dispute with Köln's new manager Zvonimir Soldo.The 2010–11 season was his best season in the Bundesliga as Köln finished 10th on the league table with Novaković scoring 17 goals, finishing the season on third place in the league's top scorer's list.