Although born in Germany, Niemeyer spent the first years of his professional career in the Netherlands, playing for FC Twente in the Eredivisie.

On 29 September 2007, Niemeyer participated in the 8–1 home crushing of Arminia Bielefeld, scoring the game opener and his first Bundesliga goal.

In the 2008–09 season, Niemeyer appeared in a career-best 25 official games, including five in the UEFA Cup, as Werder reached the final against Shakhtar Donetsk, where he started in a 2–1 overtime loss.

[2] On 1 September 2018, after the closing of the 2018 summer transfer window, he announced he had not received an offer to renew his contract and would leave the club.

At the same time he worked as the assistant coach of the first team under manager Gonzalo García and functioned as head of the youth department.