Baumgartner became head coach of Austria Wien on 27 May 2014 and had his first training session on 10 June 2014. The style he wanted to implement was an aggressive pressing. 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. After the win in the Austrian Cup, Baumgartner failed to win any of his first seven matches in the Bundesliga. His league record at this point was five draws and two losses. His first league win came against Ried which finished 3–1. Baumgartner was sacked on 22 March 2015 after a 1–0 loss to Ried the previous day. Andreas Ogris was appointed as head coach for the remainder of the season. Baumgartner was the fifth coach since the club sacked Karl Daxbacher in 2011 and the 31st coach since 1990.
Austria Salzburg
On 18 December 2015, Baumgartner was unveiled as the new head coach and sports director of Austria Salzburg. He finished the first season with a record of three wins, five draws, and nine losses in 17 matches.
SV Mattersburg
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.