Ahead of the 2013/14 season, Werner was hired as youth coach at his former club, Holstein Kiel. More precisely, he became assistant coach for the club's U16 team.[2] For the 2014/15 season, he became assistant to Christian Riecks at the second team, which played in the fifth-tier Oberliga Schleswig-Holstein. He succeeded Riecks in November 2014[3] and finished the season with the team in 2nd place. This was followed by 3rd place in the 2015/16 season.
On 17 August 2016, following the dismissal of Karsten Neitzel, Werner became head coach of Holstein Kiel as interim manager. He managed two matches, first in the Schleswig-Holstein Cup quarter-final against ETSV Weiche which finished as a 2–0 win. He also managed a 3. Liga match against FSV Zwickau, which finished as a 3–0 win.[4] On 27 August, he was replaced by Markus Anfang and returned to the second team, with whom he finished the 2016/17 season in 2nd place.
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.[6] He ultimately finished the 2019/20 season with Kiel in a safe 11th place. He resigned as coach of Holstein Kiel in September 2021 after four losses in seven games.[7]
On 28 November 2021, Werner was named the new manager of Werder Bremen as successor to Markus Anfang, who had resigned.[8][9] The newly relegated Bundesliga side were in 10th place with 20 points after matchday 15. Werner won the first 7 games with his new team and led them to 2nd place. Bremen were able to defend this position, meaning that at the end of the season they were directly promoted back to the Bundesliga for the 2022/23 season with 63 points behind FC Schalke 04.
