In the beginning of 2002, Magnin made his biggest career move by joining Bundesliga side Werder Bremen for the transfer sum of approximately 1 million Swiss Francs.

He won the double of Bundesliga and DFB-Pokal with the Northern German side in 2004, but had bad luck with many injuries and played only 45 games in four years in Bremen.

[4] When his starting position in the team began to erode in the beginning of the 2009–10 season, Magnin decided to leave Stuttgart in order to keep his chances of playing for the Swiss national squad at the 2010 World Cup.

Magnin was initially omitted from the Switzerland squad for the 2010 World Cup but was later called up to replace the injured Christoph Spycher.

On 20 February 2018, Magnin was announced as the new head coach of Swiss Super League club FC Zürich, replacing Ulrich Forte.

[10] On 20 May 2022, after a crucial 2–1 win over WSG Tirol, Altach avoided relegation by finishing one point ahead of Admira Wacker Mödling.