[2] He then became the head coach for the reserve team for Red Bull Salzburg from 8 April 2011 to 31 December 2011.

[6] Baumgartner brought St. Pölten to the Austrian Cup final during the 2013–14 season[7] after defeating Sturm Graz 1–0 in extra time in the semi–final[8] and qualified for the Europa League.

[10] His first competitive match in–charge at the club was a 6–0 win in the first round of the Austrian Cup against First Vienna FC.

[16] On 18 December 2015, Baumgartner was unveiled as the new head coach and sports director of Austria Salzburg.

[18] Baumgartner was appointed as the new manager of SV Mattersburg on 2 January 2017 bringing with him the greek defender Angelos Bountalis and a couple of other players.