Prödl made his Werder Bremen debut in the first round of the DFB-Pokal in a 9–3 win over Eintracht Nordhorn on 9 August 2008. A week later, he made his league debut for the club, in a 2–2 draw against Arminia Bielefeld. He made his Champions League debut, playing as a right-back, in a 1–1 draw against Inter Milan on 1 October 2008. By the first half of the season, he had appeared in 13 of 17 league matches, also playing in the unfamiliar right-back role in absence of Clemens Fritz. In the last match of the first half of the season he injured his ankle which saw him out for two months. On 7 March 2009, after making the bench in three matches, Prödl returned to the first team in a 0–0 draw against Hoffenheim. He scored his first Werder Bremen goal in the second leg of the last 16 of the UEFA Cup in a 2–2 draw against Saint-Étienne, from which the club progressed winning 3–2 on aggregate. Upon his return he reverted to centre-back going on to make a total of 22 appearances in his first season. Prödl formed a partnership with Naldo in central defence when they beat Bayer Leverkusen 1–0 in the DFB-Pokal Final. He also featured in the UEFA Cup final, playing the full 120 minutes in a 3–2 loss against Shakhtar Donetsk.