[1] Müller began his coaching career in November 2011, when he was appointed manager of Landesliga club TuS Tengern.
[2] He left the position in June 2012, to join SC Paderborn 07 as manager of the club's youth academy and head coach of the U23/reserve squad.
[3] On 5 May 2013, Müller took over as interim coach of SC Paderborn's professional team for the rest of the season, following the dismissal of Stephan Schmidt.
On 6 October 2015, Müller once again took charge of Paderborn's professional team on interim basis, following the departure of Markus Gellhaus.
[9] At the end of January 2017 it was confirmed, that Müller from the upcoming 2017-18 season would take charge of Arminia Bielefeld's U23/reserve team.