Müller had played at several smaller clubs at youth level, before joining the reigning German champions FSV Frankfurt in 1998.

Because many of club's star players, such as Birgit Prinz and Sandra Smisek, had left that summer, Müller immediately became a regular starter and helped the team avoid relegation.

With 36 goals, Müller was the second Bundesliga top-scorer the following season, helping Wolfsburg to achieve immediate promotion back to the German top flight.

Müller remained with Wolfsburg in their 2012–13 breakout season, when they won a treble of Bundesliga, DFB-Pokal and UEFA Women's Champions League.

In May 2013's Champions League final at Stamford Bridge Müller scored the decisive penalty kick to defeat Olympique Lyonnais 1–0.