In the 2008 state election, Müller failed to be elected to the Landtag; despite this, she was once again chosen as Minister of State for Federal and European Affairs by newly elected Minister-President Horst Seehofer in the cabinet of his coalition government, composed of members of the CSU and their junior coalition partner, the Free Democratic Party (FDP). Following the result of the 2013 state election, which resulted in Müller's election to the Landtag 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.