New signings
- Jean Zimmer (1. FC Kaiserslautern)
- Simon Terodde (VfL Bochum)
- Marcin Kaminski (Lech Posen)
- Benjamin Uphoff (U23)
- Matthias Zimmermann (U23)
- Jens Grahl (TSG Hoffenheim)
- Hajime Hosogai (Hertha BSC)
- Tobias Werner (FC Augsburg)
- Hans Nunoo Sarpei (Liberty Professionals Accra)
- Takuma Asano (FC Arsenal, on loan)
- Benjamin Pavard (OSC Lille)
- Carlos Mané (Sporting Lissabon, on loan)
- Julian Green (FC Bayern Munich, December 2016)
- Ebenezer Ofori (AIK Solna, january 2017)
- Josip Brekalo (VfL Wolfsburg, january 2017, on loan)
- Jérôme Onguéné (FC Sochaux, january 2017)
Departures
- Daniel Schwaab (leaked contract)
- Georg Niedermeier (leaked contract)
- Martin Harnik (leaked contract)
- Daniel Didavi (VfL Wolfsburg)
- Timo Werner (RB Leipzig)
- Federico Barba (FC Empoli, end of loan)
- Artem Kravets (Dynamo Kiew, end of loan)
- Lukas Rupp (TSG Hoffenheim)
- Przemyslaw Tyton (Deportivo La Coruna)
- Arianit Ferati (Hamburger SV)
- Serey Dié (FC Basel 1893)
- Filip Kostic (Hamburger SV)
- Jan Kliment (Brödby IF, on loan)
- Stephen Sama (SpVgg Greuther Fürth, January 2017)
- Philip Heise (SG Dynamo Dresden, January 2017)
- Toni Sunjic (US Palermo, January 2017, on loan)
- Kevin Großkreutz (left VfB, March 2017)
- Hajime Hosgai (Kashiwa Reysol, March 2017)