Rosenberg started the 2008–09 season well when he scored four goals and set up Hugo Almeida twice in a 9–3 win over Eintracht Nordhorn in the first round of the DFB-Pokal on 9 August 2008. Seven days later, on 16 August 2008, Rosenberg scored a brace on his debut of the season in a 2–2 against Arminia Bielefeld. A month later, on 20 September 2008, he scored twice in a 5–2 win over Bayern Munich, marking the first time Bremen defeated Bayern at the Allianz Arena. This was followed up by scoring his ninth goal of the season, in a 2–1 win against Erzgebirge Aue in the second round of the DFB-Pokal. After the start of the 2008–09 season, Rosenberg continued to remain involved in the first team despite the new arrival of Claudio Pizarro. Despite a muscular injury sustained while on international duty, Rosenberg later added two more goals by end of 2008, scoring against Hertha BSC and Inter Milan (despite a 2–1 victory, Werder Bremen were eliminated from the group stage and demoted to the UEFA Cup). On 15 March 2009, Rosenberg scored twice in a 4–0 win over VfB Stuttgart, ending his ten matches without scoring a goal. Despite being sidelined later in the 2008–09 season, he started in the 2009 UEFA Cup Final against Shakhtar Donetsk and played 78 minutes before being substituted, as Werder Bremen went on to lose 2–1 at extra time. While not winning the UEFA Cup, the club, nevertheless, won the DFB-Pokal after beating Bayer Leverkusen 1–0. By the end of the 2008–09 season, he had made 47 appearances scoring 13 times in all competitions, making him the club's third highest goal scorer, behind Claudio Pizarro and Diego. However, his goal scoring form came under criticism, due to performance expectations in the first two seasons at Werder Bremen.