| 06 Oct 20 | A. Fein Adrian Fein |  Bayern MunichMUN | → |  PSV EindhovenPSV | Loan |
| 06 Oct 20 | A. Fein Adrian Fein | Bayern MunichMUN | → | PSV EindhovenPSV | Loan |
| 05 Oct 20 | D. Costa Douglas Costa |  JuventusJUV | → | Bayern MunichMUN | Loan |
| 05 Oct 20 | B. Sarr Bouna Sarr |  MarseilleMAR | → | Bayern MunichMUN | Undisclosed |
| 05 Oct 20 | M. Cuisance Michaël Cuisance | Bayern MunichMUN | → | MarseilleMAR | Loan |
| 05 Oct 20 | D. Costa Douglas Costa | JuventusJUV | → | Bayern MunichMUN | Loan |
| 05 Oct 20 | E. Choupo-Moting Eric Maxim Choupo-Moting | XXX | → | Bayern MunichMUN | Free |
| 05 Oct 20 | B. Sarr Bouna Sarr | MarseilleMAR | → | Bayern MunichMUN | Undisclosed |
| 05 Oct 20 | M. Cuisance Michaël Cuisance | Bayern MunichMUN | → | MarseilleMAR | Loan |
| 04 Oct 20 | M. Roca Marc Roca |  EspanyolESP | → | Bayern MunichMUN | Undisclosed |
| 03 Oct 20 | S. Ulreich Sven Ulreich | Bayern MunichMUN | → |  Hamburg SVHSV | Undisclosed |
| 18 Sept 20 | T. Alcántara Thiago Alcántara | Bayern MunichMUN | → |  LiverpoolLIV | Undisclosed |
| 18 Sept 20 | T. Alcántara Thiago Alcántara | Bayern MunichMUN | → | LiverpoolLIV | Undisclosed |
| 28 Aug 20 | Barry Hepburn |  CelticCEL | → | Bayern MunichMUN | Undisclosed |
| 28 Aug 20 | Barry Hepburn | CelticCEL | → | Bayern MunichMUN | Undisclosed |
| 07 Aug 20 | C. Früchtl Christian Früchtl | Bayern MunichMUN | → |  NurnbergNUR | Loan |
| 21 Jul 20 | L. Mai Lukas Mai | Bayern MunichMUN | → |  SV Darmstadt 98DRM | Loan |
| 03 Jul 20 | L. Sané Leroy Sané |  Manchester CityMNC | → | Bayern MunichMUN | Undisclosed |
| 03 Jul 20 | L. Sané Leroy Sané | Manchester CityMNC | → | Bayern MunichMUN | Undisclosed |
| 01 Jul 20 | T. Kouassi Tanguy Kouassi |  Paris Saint-Germain PSG | → | Bayern MunichMUN | Free |
| 01 Jul 20 | A. Nübel Alexander Nübel |  Schalke 04SCHA | → | Bayern MunichMUN | Free |
| 01 Jul 20 | T. Kouassi Tanguy Kouassi | Paris Saint-Germain PSG | → | Bayern MunichMUN | Free |
| 22 Jan 20 | Á. Odriozola Álvaro Odriozola |  Real MadridMAD | → | Bayern MunichMUN | Loan |
| 22 Jan 20 | N. Kühn Nicolas Gerrit Kühn |  Ajax AmsterdamAJA | → | Bayern MunichMUN | Loan |
| 22 Jan 20 | N. Kühn Nicolas Gerrit Kühn | Ajax AmsterdamAJA | → | Bayern MunichMUN | Loan |
| 22 Jan 20 | Á. Odriozola Álvaro Odriozola | Real MadridMAD | → | Bayern MunichMUN | Loan |