In the 2016–17 season, Frankfurt managed to finish mid-table in 11th position, as well as notably reaching the 2017 DFB-Pokal Final, club's first final since 2006, where Frankfurt lost 1–2 against Borussia Dortmund. In the 2017–18 season, Frankfurt competed for a place in European competition for the following season. Kovač has typically used a 3–4–2–1 formation with emphasis on defensive stability and wing play. He took Frankfurt to the 2018 DFB-Pokal Final, the second in succession for the club, where he beat his future employer, Bayern Munich. With that win, Kovač led Frankfurt to its first trophy since 1988. He finished with a record of 38 wins, 20 draws, and 33 losses in 91 matches. Adi Hütter became his successor.