| 2026-10-30 | Bajung Darboe | Bayern München → Darboe Bajung | Free agent |
| 2026-10-30 | B. Schmitz | Bayern München → Schmitz Benno | Free agent |
| 2026-10-30 | Benedikt Wimmer | Bayern München → Wimmer Benedikt | Free agent |
| 2026-10-30 | T. Buchmann | Bayern München → Buchmann Tarek | Free agent |
| 2026-10-30 | Mudaser Sadat | Bayern München → Sadat Mudaser | Free agent |
| 2026-10-30 | M. Scott | Bayern München → Scott Michael | Free agent |
| 2026-08-31 | A. Ibrahimović | Bayern München → FC Augsburg | Loan |
| 2026-08-30 | Gibson Nana Adu | Bayern München → Adu Gibson | Free agent |
| 2026-08-27 | L. Goretzka | Bayern München → Aston Villa | Free agent |
| 2026-08-26 | Bryan Zaragoza | Bayern München → Espanyol | Loan |
| 2026-08-26 | W. Mike | Bayern München → Club Brugge KV | Transfer |
| 2026-08-25 | João Palhinha | Bayern München → Benfica | Transfer |
| 2026-08-25 | F. Chávez | Bayern München → 1. FC Magdeburg | Loan |
| 2026-08-12 | A. Sieb | Bayern München → Los Angeles FC | Transfer |
| 2026-08-09 | Bara Ndiaye | Gambinos Stars → Bayern München | Transfer |
| 2026-07-17 | N. Aséko Nkili | Bayern München → Eintracht Frankfurt | Transfer |
| 2026-07-15 | L. Zvonarek | Bayern München → Estrela | Transfer |
| 2026-07-12 | Jonathan Asp Jensen | Bayern München → Deportivo La Coruna | Transfer |
| 2026-07-07 | A. Nübel | Bayern München → Beşiktaş | Transfer |
| 2026-07-03 | D. Ofli | Bayern München → Karlsruher SC | Loan |
| 2026-07-02 | N. Brown | Eintracht Frankfurt → Bayern München | Transfer |
| 2026-07-01 | N. Aséko Nkili | Hannover 96 → Bayern München | Transfer |
| 2026-06-30 | M. Krattenmacher | Bayern München → SV Elversberg | Transfer |
| 2026-06-30 | Daniel Peretz | Bayern München → Southampton | Transfer |
| 2026-06-30 | M. Schmitt | Bayern München → SSV Jahn Regensburg | Transfer |
| 2026-06-30 | Grayson Dettoni | Bayern München → SV Darmstadt 98 | Transfer |
| 2026-06-30 | J. Kusi-Asare | Bayern München → Fulham | Transfer |
| 2026-06-30 | P. Scholl | Bayern München → Karlsruher SC | Transfer |
| 2026-06-30 | Robert Deziel | Bayern München → Legia Warszawa | Free agent |
| 2026-06-30 | B. Hepburn | Bayern München → Stirling Albion | Free agent |
| 2026-06-30 | N. Aséko Nkili | Bayern München → Hannover 96 | Transfer |
| 2026-06-30 | I. Saibari | PSV Eindhoven → Bayern München | Transfer |
| 2026-06-29 | Gibson Nana Adu | SCR Altach → Bayern München | Return from loan |
| 2026-06-29 | M. Krattenmacher | Hertha BSC → Bayern München | Return from loan |
| 2026-06-29 | L. Zvonarek | Grasshoppers → Bayern München | Return from loan |
| 2026-06-29 | A. Ibrahimović | 1. FC Heidenheim → Bayern München | Return from loan |
| 2026-06-29 | A. Nübel | Bayern München → Beşiktaş | Transfer |
| 2026-06-29 | A. Nübel | VfB Stuttgart → Bayern München | Return from loan |
| 2026-06-29 | A. Sieb | FSV Mainz 05 → Bayern München | Return from loan |
| 2026-06-29 | Daniel Peretz | Southampton → Bayern München | Return from loan |
| 2026-06-29 | Bryan Zaragoza | AS Roma → Bayern München | Return from loan |
| 2026-06-29 | L. Goretzka | Bayern München → Goretzka Leon | Free agent |
| 2026-06-29 | João Palhinha | Tottenham → Bayern München | Return from loan |
| 2026-06-29 | S. Boey | Galatasaray → Bayern München | Return from loan |
| 2026-06-29 | Raphaël Guerreiro | Bayern München → Guerreiro Raphael | Free agent |
| 2026-06-29 | Jonathan Asp Jensen | Grasshoppers → Bayern München | Return from loan |
| 2026-06-29 | F. Chávez | 1. FC Köln → Bayern München | Return from loan |
| 2026-06-29 | M. Schmitt | SSV Ulm 1846 → Bayern München | Return from loan |
| 2026-06-29 | Benedikt Wimmer | SV Sandhausen → Bayern München | Return from loan |
| 2026-06-29 | Bara Ndiaye | Bayern München → Gambinos Stars | Return from loan |
| 2026-06-29 | J. Fernandez | 1. FC Nürnberg → Bayern München | Return from loan |
| 2026-06-29 | Grayson Dettoni | SV Darmstadt 98 → Bayern München | Return from loan |
| 2026-06-29 | N. Jackson | Bayern München → Chelsea | Return from loan |
| 2026-06-29 | T. Buchmann | 1. FC Nürnberg → Bayern München | Return from loan |
| 2026-06-29 | J. Kusi-Asare | Fulham → Bayern München | Return from loan |
| 2026-06-29 | P. Scholl | Karlsruher SC → Bayern München | Return from loan |
| 2026-06-29 | N. Aséko Nkili | Hannover 96 → Bayern München | Return from loan |
| 2026-03-04 | M. Cardozo | Bayern München → Bayern München | Raise |
| 2026-02-13 | David Emmanuel | Bayern München → Kladno | Free agent |
| 2026-02-04 | S. Boey | Bayern München → Galatasaray | Loan |
| 2026-02-03 | M. Mergner | Bayern München → First Vienna | Free agent |
| 2026-02-01 | B. Sarr | Bayern München → Metz | Free agent |
| 2026-02-01 | Bryan Zaragoza | Bayern München → AS Roma | Loan |
| 2026-02-01 | F. Chávez | Bayern München → 1. FC Köln | Loan |
| 2026-02-01 | M. Dalpiaz | Bayern München → AC Mailand | Transfer |
| 2026-01-31 | Bryan Zaragoza | Celta Vigo → Bayern München | Return from loan |
| 2026-01-31 | M. Gottlicher | Bayern München → VfL Bochum | Transfer |
| 2026-01-31 | A. Licina | Bayern München → Juventus (U23) | - |
| 2026-01-30 | J. Fernandez | Bayern München → 1. FC Nürnberg | Loan |
| 2026-01-30 | Grayson Dettoni | Bayern München → SV Darmstadt 98 | Loan |
| 2026-01-29 | D. Jonathans | Bayern München → AS Jeunesse Esch | Free agent |
| 2026-01-29 | Mudaser Sadat | SKU Amstetten → Bayern München | Return from loan |
| 2026-01-07 | Daniel Peretz | Bayern München → Southampton | Loan |
| 2026-01-06 | Daniel Peretz | Hamburger SV → Bayern München | Return from loan |
| 2026-01-06 | M. Popovic | Bayern München → Vancouver Whitecaps II | - |
| 2026-01-02 | Bara Ndiaye | Gambinos Stars → Bayern München | Loan |