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. In the opening game of the 2009–10 season, Prödl played as a centre-back in a 3–2 loss against Eintracht Frankfurt and was sent-off in the last minutes after a second bookable offence. Soon after, he suffered a knee injury. After three months on the sidelines, he appeared on the substitution bench and made his return to the first team coming on for Naldo in the 76th minute of a 6–0 win over Freiburg on 21 November 2009. He scored his first Werder Bremen league goal on 27 February 2010, in a 2–1 win over Mainz 05. Prödl spent most of the season on the substitution bench making nine appearances for the club. In the 2010–11 season, Prödl became a regular starter following Naldo's injury at the start of the season and formed a partnership in central defence with Per Mertesacker. He scored his first European goal on matchday 6 of the Champions League group stage in a 3–0 win over Inter Milan on 7 December 2010. He scored his first league goal of the season on 27 February 2011 in a 2–2 draw against Bayer Leverkusen. Having suffered a knee injury and undergone surgery it was announced in March 2011 that Prödl would miss the remainder of the 2010–11 season. He ended season with 25 appearances. At the start of the 2011–12 season, Prödl remained a regular starter. He scored his first goal of the season in a 3–1 win over Mainz on 29 October 2011. On 21 January 2012, during a match against Kaiserslautern, he was substituted off with an injury in the 29th minute. After a successful surgery, it was announced that he would be out for six weeks. Prödl made his return against Hannover 96 on 11 March 2012 scoring in a 3–0 win. However, his return was short-lived as he suffered a hamstring injury which kept him out for two weeks. He made his return to the