| 01 Sept 25 | J. Kusi-Asare Jonah Kusi-Asare |  Bayern MunichMUN | → |  FulhamFUL | Loan |
| 01 Sept 25 | N. Jackson Nicolas Jackson |  ChelseaCHE | → | Bayern MunichMUN | Loan |
| 22 Aug 25 | P. Wanner Paul Wanner | Bayern MunichMUN | → |  PSV EindhovenPSV | Undisclosed |
| 15 Aug 25 | K. Coman Kingsley Coman | Bayern MunichMUN | → |  Al NassrNSR | Undisclosed |
| 06 Aug 25 | T. Müller Thomas Müller | Bayern MunichMUN | → |  Vancouver WhitecapsVAN | Free |
| 05 Aug 25 | T. Buchmann Tarek Buchmann | Bayern MunichMUN | → |  1. FC NürnbergFCN | Loan |
| 03 Aug 25 | J. Palhinha João Palhinha | Bayern MunichMUN | → |  Tottenham HotspurTOT | Loan |
| 30 Jul 25 | L. Díaz Luis Díaz |  LiverpoolLIV | → | Bayern MunichMUN | Undisclosed |
| 30 Jul 25 | B. Zaragoza Bryan Zaragoza | Bayern MunichMUN | → |  Celta VigoCEL | Loan |
| 29 Jul 25 | A. Aznou Adam Aznou | Bayern MunichMUN | → |  EvertonEVE | Undisclosed |
| 29 Jul 25 | L. Zvonarek Lovro Zvonarek | Bayern MunichMUN | → |  GrasshoppersGCZ | Loan |
| 21 Jul 25 | D. Peretz Daniel Peretz | Bayern MunichMUN | → |  Hamburg SVHSV | Loan |
| 18 Jul 25 | N. Irankunda Nestory Irankunda | Bayern MunichMUN | → |  WatfordWAT | Undisclosed |
| 01 Jul 25 | E. Dier Eric Dier | Bayern MunichMUN | → |  AS MonacoMON | Free |
| 01 Jul 25 | M. Tel Mathys Tel | Bayern MunichMUN | → | Tottenham HotspurTOT | Undisclosed |
| 01 Jul 25 | M. Krattenmacher Maurice Krattenmacher | Bayern MunichMUN | → |  Hertha BerlinBSC | Loan |
| 01 Jul 25 | L. Sané Leroy Sané | Bayern MunichMUN | → |  GalatasarayGAL | Free |
| 01 Jul 25 | A. Ibrahimovic Arijon Ibrahimovic | Bayern MunichMUN | → |  1. FC Heidenheim 1846HDH | Loan |
| 01 Jul 25 | G. Vidovic Gabriel Vidovic | Bayern MunichMUN | → | DZXDinamo ZagrebDinamo Zagreb | Undisclosed |
| 09 Jun 25 | J. Tah Jonathan Tah |  Bayer LeverkusenB04 | → | Bayern MunichMUN | Undisclosed |
| 09 Jun 25 | T. Bischof Tom Bischof |  TSG HoffenheimTSG | → | Bayern MunichMUN | Undisclosed |
| 03 Feb 25 | A. Aznou Adam Aznou | Bayern MunichMUN | → |  Real ValladolidVLL | Loan |
| 03 Feb 25 | N. Aséko Noël Aséko | Bayern MunichMUN | → |  Hannover 96H96 | Loan |
| 27 Jan 25 | J. Urbig Jonas Urbig |  FC CologneKOE | → | Bayern MunichMUN | Undisclosed |
| 13 Jan 25 | A. Ibrahimovic Arijon Ibrahimovic | Bayern MunichMUN | → |  LazioLAZ | Loan |
| 03 Jan 25 | F. Krätzig Frans Krätzig | Bayern MunichMUN | → | 1. FC Heidenheim 1846HDH | Loan |
| 01 Jan 25 | B. Darboe Bajung Darboe |  LAFCLAFC | → | Bayern MunichMUN | Undisclosed |