Compper started the 2008–09 season when he helped the club win the first Bundesliga match, in a 3–0 win over Energie Cottbus. He continued to remain his first team, playing in the centre–back position. On 27 September 2008, he scored his first goal in a 5–4 loss against Werder Bremen. He helped the side with wins that led to them being at the top of the table until January. However, the club's form soon suffered that ended up losing their spot at the top of the table and Compper, himself, suffered setbacks despite having playing time. He captained the side for the first time on 2 May 2009, where he played the whole game, in a 4–0 loss against Wolfsburg. Despite being further setbacks during the 2008–09 season, Compper finished his full season at the club, making the total of 32 appearances and scoring once in all competitions.