Towards the end of his playing career, he was a player-manager for FC Carl Zeiss Jena in the 1998–99 season.

After the end of his contract in Schönberg, he became the new assistant manager of Austrian club SK Sturm Graz.

[1] His contract ran until 30 June 2010, but on 11 March 2010 Arminia Bielefeld officials dismissed Gerstner.

The team was then managed by caretakers Frank Eulberg and Jörg Böhme until the end of the season.

[2] On 28 February 2011, Gerstner took over Kickers Offenbach,[3] but he was fired after two months due to lack of success.