She has held a wide range of public positions at the municipal, state, and European Parliamentary level since beginning her political career in 1990.

After succeeding Stoiber as Minister-President, Günther Beckstein appointed Müller as Minister of Economy, Infrastructure, Transport and Technology on 16 October 2007.

Following the result of the 2013 state election, which resulted in Müller's election to the Landtag[2] and an absolute majority for the CSU, she was appointed to the 2nd Seehofer Cabinet as Minister of Labor and Social Affairs, Family and Integration, replacing fellow party member Christine Harderthauer.

In her position as Minister of Labor and Social Affairs, Family and Integration, Müller was criticized for the remarks she made when visiting a newly opened detention center near Ingolstadt in 2015.

But you know that you have to go back”, a remark criticized by the Süddeutsche Zeitung as depicting a “complete lack of empathy for fleeing people”.