Ahead of the 2013/14 season, Werner was hired as youth coach at his former club, Holstein Kiel.

On 17 August 2016, following the dismissal of Karsten Neitzel, Werner became head coach of Holstein Kiel as interim manager.

On 16 September 2019, Werner returned as the interim manager for Kiel, which was in 16th place with five points after matchday 6, following the dismissal of André Schubert.

[5] On 24 October 2019, After six points from four games, he was permanently appointed as manager of Holstein Kiel, signing a deal until June 2022.

[7] On 28 November 2021, Werner was named the new manager of Werder Bremen as successor to Markus Anfang, who had resigned.