FC Bayern II: every transfer in and out, fees paid and earned, squad market value, €5.3m spent and €16m earned.
| Date | Player | From | To | Fee |
|---|---|---|---|---|
| 2026-07-01 | Jussef Nasrawe | FC Bayern II | SV Ried | €100k |
| 2026-02-02 | Felipe Chávez | FC Bayern II | 1.FC Köln | Loan |
| 2026-01-23 | Jussef Nasrawe | FC Bayern II | SV Ried | Loan |
| 2026-01-01 | David Santos Daiber | FC Bayern U19 | FC Bayern II | — |
| 2025-08-01 | Jonathan Asp Jensen | FC Bayern II | Grasshoppers | Loan |
| 2025-07-23 | Hyun-ju Lee | FC Bayern II | Arouca | €1.5m |
| 2025-07-18 | Nestory Irankunda | FC Bayern II | Watford | €3m |
| 2025-07-15 | Tom Ritzy Hülsmann | FC Bayern II | TSV Hartberg | — |
| 2025-07-02 | Maximilian Hennig | FC Bayern II | TSV Hartberg | Loan |
| 2025-07-01 | Maximilian Hennig | FC Bayern U19 | FC Bayern II | — |
| 2025-07-01 | Max Scholze | FC Bayern II | SSV Ulm 1846 | — |
| 2025-07-01 | Max Schmitt | FC Bayern II | SSV Ulm 1846 | Loan |
| 2025-07-01 | Matteo Pérez Vinlöf | FC Bayern II | Dinamo Zagreb | €2m |
| 2025-07-01 | Leon Klanac | FC Bayern U19 | FC Bayern II | — |
| 2025-07-01 | Jussef Nasrawe | FC Bayern U19 | FC Bayern II | — |
| 2025-07-01 | Jonah Kusi-Asare | FC Bayern II | Bayern Munich | — |
| 2025-07-01 | Emirhan Demircan | FC Bayern II | Utrecht | Free |
| 2025-02-03 | Taichi Fukui | FC Bayern II | Arouca | €1.6m |
| 2025-02-03 | Noel Aseko | FC Bayern II | Hannover 96 | Loan |
| 2025-01-04 | Nestory Irankunda | FC Bayern II | Grasshoppers | Loan |