Baumann started his coaching career at Rot-Weiß Erfurt when he was hired on 19 February 2008.[4] His first match as head coach was a 5–0 win against the reserve team of VfL Wolfsburg on 23 February 2008.[5] He finished the 2007–08 season in seventh place and promotion to the first ever3. Liga season.[6] Baumann was sacked on 28 April 2009,[7] three days after Rot-Weiß Erfurt lost to Kickers Emden 1–0.[8]
Then on 22 February 2012, Erzgebirge Aue hired Baumann as head coach after Rico Schmitt was sacked the previous day.[13] His first match as head coach of Erzgebirge Aue was a 2–0 loss to Energie Cottbus.[14] He was sacked on 28 April 2013.[15] His final match was a 0–0 draw against MSV Duisburg.[16]
He then took over the job at Duisburg on 8 July 2013.[17] On 15 April 2014, Duisburg announced that Baumann wouldn't return for another season[18] and had his final match on 15 May 2014 in the state cup final which Duisburg won 5–2.[19]
On 9 December 2014, he was hired as the head coach of Hansa Rostock.[20] He was sacked on 5 December 2015.[21]