Striker Nils Petersen will remain in Bremen and not return to Bayern Munich after signing a four-year deal with Werder on Thursday.
Petersen, who spent the past season on loan to Werder, scored 11 goals in the Bundesliga last season.
Petersen says he is "very pleased that things turned out the way I had wished for."
Werder barely escaped relegation and is rebuilding after parting company with long-term coach Thomas Schaaf. The club wants to sign Robin Dutt, the director of sports with the German Football Federation.
No details of the deal between Werder and Bayern were disclosed.