He continued to feature regularly for Werder, although he struggled with injuries in his later years. Baumann scored the goal that took Bremen to the 2009 UEFA Cup Final, in the second leg of the semifinal against Hamburger SV, from a corner conceded by after the ball had deflected off a crumpled up piece of paper thrown from the home supporters. He announced his retirement on 20 May 2009, as his contract was to expire the following month.