| Player | Reason | From | Until | Days | Games missed |
|---|---|---|---|---|---|
 Assan Ouédraogo | Shoulder Injury | 14 Sept 2026 | Current | — | 0 |
| Assan Ouédraogo | Fitness | 9 Sept 2026 | — | — | 0 |
| Assan Ouédraogo | Fitness | 9 Sept 2026 | — | — | 1 |
 Castello Lukeba | Muscular Problems | 4 Sept 2026 | 6 Sept 2026 | 2 | 1 |
 Rocco Reitz | Hamstring Injury | 3 Sept 2026 | Current | — | 3 |
| Assan Ouédraogo | Fitness | 3 Sept 2026 | 8 Sept 2026 | 5 | 1 |
 Brajan Gruda | Ankle Injury | 30 Aug 2026 | 6 Sept 2026 | 7 | 1 |
 Ørjan Nyland | Foot Injury | 20 Aug 2026 | 3 Sept 2026 | 14 | 2 |
 Rômulo | Tendon Irritation | 14 Aug 2026 | 4 Sept 2026 | 21 | 4 |
 Maxime Estève | Thigh Problems | 12 Aug 2026 | 24 Aug 2026 | 12 | 2 |
| Assan Ouédraogo | Shoulder Injury | 8 Aug 2026 | 1 Sept 2026 | 24 | 4 |
 Lukas Klostermann | Groin Problems | 5 Aug 2026 | 18 Aug 2026 | 13 | — |
 Christoph Baumgartner | Hamstring Injury | 1 Jun 2026 | Current | 152 | 10 |
 Unknown player | Ankle Problems | 7 May 2026 | 30 Jun 2026 | 54 | 3 |
 Nicolas Seiwald | Infection | 23 Apr 2026 | 28 Apr 2026 | 5 | 1 |
 David Raum | Groin Problems | 20 Apr 2026 | 29 Apr 2026 | 9 | 1 |
| Castello Lukeba | Adductor Pain | 19 Apr 2026 | 29 Apr 2026 | 10 | 1 |
 Ezechiel Banzuzi | Capsular Injury | 14 Apr 2026 | 11 May 2026 | 27 | 4 |
 Willi Orbán | Muscular Problems | 12 Apr 2026 | 20 Apr 2026 | 8 | 1 |
 Conrad Harder | Thigh Problems | 9 Apr 2026 | 15 Apr 2026 | 6 | 1 |
| Castello Lukeba | Adductor Injury | 5 Apr 2026 | 17 Apr 2026 | 12 | 1 |
 Suleiman Sani | Hip Injury | 2 Apr 2026 | 7 May 2026 | 35 | 5 |
 Leopold Zingerle | Hand Injury | 2 Apr 2026 | 9 Aug 2026 | 129 | 12 |
| Brajan Gruda | Adductor Pain | 31 Mar 2026 | 10 Apr 2026 | 10 | 1 |
 Xaver Schlager | Adductor Pain | 22 Feb 2026 | 12 Mar 2026 | 18 | 2 |
 Unknown player | Back Problems | 19 Feb 2026 | 23 Mar 2026 | 32 | 5 |
 Péter Gulácsi | Inner Knee Ligament Tear | 16 Feb 2026 | 2 Apr 2026 | 45 | 5 |
| Unknown player | ILL | 2 Feb 2026 | 9 Feb 2026 | 7 | 0 |
| Suleiman Sani | Ankle Injury | 29 Jan 2026 | 2 Mar 2026 | 32 | 6 |
 Johan Bakayoko | Fitness | 26 Jan 2026 | 28 Jan 2026 | 2 | 0 |
| Castello Lukeba | Knee Problems | 22 Jan 2026 | 9 Feb 2026 | 18 | 3 |
| Assan Ouédraogo | Knee Injury | 15 Jan 2026 | 31 Mar 2026 | 75 | 12 |
| Suleiman Sani | Fitness | 13 Jan 2026 | 19 Jan 2026 | 6 | 2 |
 Benjamin Henrichs | Fitness | 3 Jan 2026 | 15 Jan 2026 | 12 | 1 |
| Lukas Klostermann | Flu | 30 Dec 2025 | 19 Jan 2026 | 20 | 2 |
| Johan Bakayoko | Muscular Problems | 18 Dec 2025 | 25 Jan 2026 | 38 | 3 |
| Ezechiel Banzuzi | Muscle Injury | 11 Dec 2025 | 7 Jan 2026 | 27 | 2 |
 Antonio Nusa | Ankle Injury | 7 Dec 2025 | 11 Jan 2026 | 35 | 2 |
| Johan Bakayoko | Muscular Problems | 2 Dec 2025 | 4 Dec 2025 | 2 | 1 |
 Unknown player | Muscular Problems | 1 Dec 2025 | 8 Dec 2025 | 7 | 2 |
 Ridle Baku | Ankle Injury | 29 Nov 2025 | 18 Dec 2025 | 19 | 4 |
| Assan Ouédraogo | Knee Injury | 24 Nov 2025 | 2 Jan 2026 | 39 | 5 |
| Rômulo | Tendon Irritation | 21 Nov 2025 | 18 Dec 2025 | 27 | 5 |
 Unknown player | Hamstring Injury | 19 Nov 2025 | 15 Dec 2025 | 26 | 5 |
| Xaver Schlager | Calf Problems | 8 Nov 2025 | 12 Nov 2025 | 4 | 1 |
 Max Finkgräfe | Fitness | 26 Oct 2025 | 9 Nov 2025 | 14 | 3 |
 Viggo Gebel | Cruciate Ligament Tear | 19 Oct 2025 | 30 Jun 2026 | 254 | 31 |
 Unknown player | Infection | 3 Oct 2025 | 6 Oct 2025 | 3 | 1 |
| Unknown player | Muscular Problems | 1 Oct 2025 | 6 Oct 2025 | 5 | 1 |
| Xaver Schlager | Fitness | 25 Sept 2025 | — | — | 44 |
| Unknown player | Knee Injury | 24 Sept 2025 | 17 Nov 2025 | 54 | 7 |
| Lukas Klostermann | Muscular Problems | 18 Sept 2025 | 23 Sept 2025 | 5 | 1 |
| Max Finkgräfe | Inner Ligament Injury | 17 Sept 2025 | 26 Oct 2025 | 39 | 4 |
| Antonio Nusa | Elbow Fracture | 14 Sept 2025 | 23 Sept 2025 | 9 | 1 |
| Xaver Schlager | Muscle Injury | 14 Sept 2025 | 6 Oct 2025 | 22 | 1 |
 Amadou Haidara | Muscular Problems | 26 Aug 2025 | 29 Sept 2025 | 34 | 4 |
 Tidiam Gomis | Fitness | 22 Aug 2025 | 15 Sept 2025 | 24 | 3 |
 Andrija Maksimovic | Fitness | 21 Aug 2025 | 1 Sept 2025 | 11 | 1 |
| Max Finkgräfe | Muscular Problems | 15 Aug 2025 | 23 Aug 2025 | 8 | 2 |
| Lukas Klostermann | Calf Problems | 8 Aug 2025 | 25 Aug 2025 | 17 | 2 |
| Andrija Maksimovic | Thigh Problems | 8 Aug 2025 | 20 Aug 2025 | 12 | 1 |
| Tidiam Gomis | Inner Ligament Injury | 18 Jul 2025 | 21 Aug 2025 | 34 | 2 |
| Castello Lukeba | Abdominal Muscle Strain | 16 May 2025 | 24 May 2025 | 8 | 1 |
| Xaver Schlager | Fitness | 14 May 2025 | 19 May 2025 | 5 | 1 |
| Amadou Haidara | Inner Ligament Injury | 7 May 2025 | 30 Jun 2025 | 54 | 3 |
| Willi Orbán | Fitness | 6 May 2025 | 15 May 2025 | 9 | 1 |
| Péter Gulácsi | Concussion | 21 Apr 2025 | 5 May 2025 | 14 | 2 |
| Unknown player | Minor Knock | 17 Apr 2025 | 22 Apr 2025 | 5 | 1 |
| Assan Ouédraogo | Fitness | 15 Apr 2025 | 28 Apr 2025 | 13 | 2 |
| David Raum | Hamstring Injury | 11 Apr 2025 | 24 Apr 2025 | 13 | 2 |
| Willi Orbán | Muscular Problems | 11 Apr 2025 | 6 May 2025 | 25 | 4 |
| Unknown player | ILL | 29 Mar 2025 | — | — | 59 |
| Unknown player | ILL | 28 Mar 2025 | 3 Apr 2025 | 6 | 1 |
| Péter Gulácsi | ILL | 28 Mar 2025 | 31 Mar 2025 | 3 | 1 |
| Xaver Schlager | Muscle Injury | 27 Mar 2025 | 14 May 2025 | 48 | 8 |
 Yussuf Poulsen | Muscular Problems | 14 Mar 2025 | 27 Mar 2025 | 13 | 1 |
| Christoph Baumgartner | ILL | 7 Mar 2025 | 12 Mar 2025 | 5 | 1 |
| Lukas Klostermann | ILL | 7 Mar 2025 | 12 Mar 2025 | 5 | 1 |
| Yussuf Poulsen | Knock | 21 Feb 2025 | 27 Feb 2025 | 6 | 1 |
| Antonio Nusa | Knee Injury | 10 Feb 2025 | 21 Apr 2025 | 70 | 11 |
| Yussuf Poulsen | Hamstring Injury | 5 Feb 2025 | 13 Feb 2025 | 8 | 1 |
| Unknown player | Doubtful | 29 Jan 2025 | 29 Jan 2025 | 0 | 1 |
| Unknown player | Muscular Problems | 25 Jan 2025 | 30 Jan 2025 | 5 | 1 |
 Faik Sakar | Torn Lateral Knee Ligament | 18 Jan 2025 | 25 May 2025 | 127 | 21 |
 Unknown player | Calf Problems | 15 Jan 2025 | 31 Jan 2025 | 16 | 5 |
| Xaver Schlager | Knee Problems | 7 Jan 2025 | 14 Mar 2025 | 66 | 13 |
| Benjamin Henrichs | Achilles Tendon Rupture | 21 Dec 2024 | 2 Jan 2026 | 377 | 24 |
| Castello Lukeba | Hamstring Injury | 30 Nov 2024 | 26 Jan 2025 | 57 | 9 |
| Assan Ouédraogo | Hamstring Injury | 27 Nov 2024 | 15 Apr 2025 | 139 | 24 |
| Lukas Klostermann | Muscular Problems | 25 Nov 2024 | 2 Dec 2024 | 7 | 2 |
| Unknown player | Muscle Injury | 20 Nov 2024 | 11 Dec 2024 | 21 | 6 |
| Yussuf Poulsen | Hamstring Injury | 18 Nov 2024 | 16 Jan 2025 | 59 | 9 |
 Eljif Elmas | Torn Muscle Fiber | 15 Nov 2024 | 2 Jan 2025 | 48 | 8 |
 Unknown player | Muscular Problems | 6 Nov 2024 | 22 Nov 2024 | 16 | 1 |
| Assan Ouédraogo | Doubtful | 5 Nov 2024 | 5 Nov 2024 | 0 | — |
 Loïs Openda | Doubtful | 5 Nov 2024 | 5 Nov 2024 | 0 | — |
| Nicolas Seiwald | Doubtful | 5 Nov 2024 | 5 Nov 2024 | 0 | — |
| Castello Lukeba | Muscular Problems | 1 Nov 2024 | 20 Nov 2024 | 19 | 3 |
| Loïs Openda | Knock | 27 Oct 2024 | 1 Nov 2024 | 5 | 1 |
 Xavi Simons | Ankle Injury | 24 Oct 2024 | 1 Jan 2025 | 69 | 13 |
