In July 2012, Schmidt became head coach of 1860 Munich II[5] and then became head coach of the first team on 18 November 2012, when Reiner Maurer was sacked.[6] Schmidt was sacked on 31 August 2013[7] and temporarily replaced by Markus von Ahlen as caretaker[7] and later by Friedhelm Funkel as permanent replacement.[8] On 1 July 2014, Schmidt started managing Jahn Regensburg.[9] He was sacked on 10 November 2014.[10] He was sacked by Türkgücü München in February 2021, after starting the job in the summer of 2020.[11]
On 26 April 2021, he took over the head coach position at Dynamo Dresden, originally only on a short contract until the end of the 2020–21 season.[12] However, after his team won six out of seven games without conceding a single goal and secured promotion to the 2. Bundesliga, Schmidt's contract was extended until 2023.[13] Schmidt was sacked on 1 March 2022 after seven games without a win and falling to 14th place.[14]