After the end of his playing career, Maucksch went into coaching, taking over at
Döbelner SC in early 2007. In October of the same year, he was appointed as manager of
Dynamo Dresden's reserve team, replacing
Jan Seifert, who had stepped up to the assistant manager's role. In his second season in charge, he led the team to victory in both the
Landesliga Sachsen and the
Sachsenpokal. Following this success, he was appointed as manager of Dynamo's first team in October 2009, after the sacking of
Ruud Kaiser. Maucksch managed to steer the club clear of relegation, and in the following season within an outside chance of a playoff place, but was sacked in April 2011 after a run of five games without a win. In the summer of 2018 he signed with
Sportfreunde Lotte. He was sacked after just four games on 24 August 2018. On 9 January 2019, Maucksch was appointed as the manager of
BFC Dynamo on a contract until June 2020. Just half a year later, at the end of the 2018–19 season, BFC Dynamo dissolved the contract with Matthias Maucksch by Maucksch's request. ==Honours==