| Player | Reason | From | Until | Days | Games missed |
|---|---|---|---|---|---|
 Ansgar Knauff | Cold | 18 Oct 2024 | 23 Oct 2024 | 5 | 1 |
 Hugo Ekitiké | Knock | 27 Sept 2024 | 1 Oct 2024 | 4 | 1 |
 Mario Götze | ILL | 19 Sept 2024 | 28 Sept 2024 | 9 | 2 |
 Kevin Trapp | Hamstring Injury | 15 Sept 2024 | 15 Oct 2024 | 30 | 5 |
 Oscar Højlund | Metatarsal Fracture | 28 Aug 2024 | 12 Nov 2024 | 76 | 14 |
 Nnamdi Collins | Injury | 3 May 2024 | 10 May 2024 | 7 | 1 |
 Unknown player | Heel Problems | 3 May 2024 | 3 Jul 2024 | 61 | 2 |
 Unknown player | Ankle Injury | 22 Apr 2024 | 3 May 2024 | 11 | 1 |
| Mario Götze | Eye Injury | 12 Apr 2024 | 15 Apr 2024 | 3 | 1 |
| Hugo Ekitiké | Muscular Problems | 4 Apr 2024 | 11 Apr 2024 | 7 | 1 |
 Ellyes Skhiri | Calf Problems | 4 Apr 2024 | 8 Apr 2024 | 4 | 1 |
 Unknown player | ILL | 25 Mar 2024 | 7 Apr 2024 | 13 | 2 |
 Hugo Larsson | Calf Problems | 20 Mar 2024 | 3 Apr 2024 | 14 | 1 |
 Unknown player | Hamstring Injury | 9 Mar 2024 | 25 Mar 2024 | 16 | 2 |
 Jean-Mattéo Bahoya | Calf Injury | 6 Mar 2024 | 12 Mar 2024 | 6 | 1 |
 Unknown player | Injury | 1 Mar 2024 | 20 Mar 2024 | 19 | 3 |
 Unknown player | Knee Problems | 23 Feb 2024 | 13 May 2024 | 80 | 11 |
| Ellyes Skhiri | Back Problems | 23 Feb 2024 | 1 Mar 2024 | 7 | 1 |
 Unknown player | Cruciate Ligament Tear | 19 Feb 2024 | 30 Apr 2025 | 436 | 12 |
| Unknown player | Ankle Problems | 18 Feb 2024 | 4 Mar 2024 | 15 | 2 |
 Elias Baum | ILL | 13 Feb 2024 | 16 Feb 2024 | 3 | 0 |
| Hugo Larsson | Hamstring Injury | 11 Feb 2024 | 1 Mar 2024 | 19 | 4 |
| Kevin Trapp | Back Problems | 10 Feb 2024 | 14 Feb 2024 | 4 | 1 |
 Junior Dina Ebimbe | Muscle Injury | 7 Feb 2024 | 13 Feb 2024 | 6 | 1 |
 Omar Marmoush | ILL | 29 Jan 2024 | 8 Feb 2024 | 10 | 1 |
 Farès Chaïbi | Cold | 13 Dec 2023 | 15 Dec 2023 | 2 | 0 |
| Omar Marmoush | ILL | 12 Dec 2023 | 16 Dec 2023 | 4 | 1 |
 Unknown player | Injury | 7 Dec 2023 | 31 Dec 2023 | 24 | 5 |
 Kristijan Jakic | Calf Injury | 6 Dec 2023 | 24 Dec 2023 | 18 | 5 |
| Ellyes Skhiri | Hamstring Injury | 1 Dec 2023 | 15 Dec 2023 | 14 | 3 |
 Timothy Chandler | Calf Injury | 29 Nov 2023 | 15 Jan 2024 | 47 | 9 |
 Unknown player | Back Problems | 24 Nov 2023 | 7 Dec 2023 | 13 | 4 |
 Unknown player | Fitness | 17 Nov 2023 | 14 Dec 2023 | 27 | 5 |
| Timothy Chandler | Cold | 8 Nov 2023 | 11 Nov 2023 | 3 | 1 |
 Robin Koch | Calf Injury | 8 Nov 2023 | 1 Dec 2023 | 23 | 3 |
 Unknown player | Shoulder Injury | 6 Nov 2023 | 10 Nov 2023 | 4 | 0 |
| Kevin Trapp | Back Problems | 31 Oct 2023 | 3 Nov 2023 | 3 | 1 |
| Mario Götze | Back Problems | 31 Oct 2023 | 3 Nov 2023 | 3 | 1 |
| Kevin Trapp | Back Problems | 18 Oct 2023 | 27 Oct 2023 | 9 | 1 |
| Unknown player | Calf Injury | 22 Sept 2023 | 15 Jan 2024 | 115 | 22 |
| Unknown player | Elbow Injury | 16 Sept 2023 | 16 Nov 2023 | 61 | 13 |
| Unknown player | ILL | 15 Sept 2023 | 18 Sept 2023 | 3 | 1 |
| Kristijan Jakic | Knee Problems | 13 Sept 2023 | 25 Oct 2023 | 42 | 7 |
| Kristijan Jakic | Concussion | 1 Sept 2023 | 7 Sept 2023 | 6 | 1 |
| Unknown player | Injury | 28 Aug 2023 | 29 Sept 2023 | 32 | 3 |
 Unknown player | ILL | 21 Aug 2023 | 28 Aug 2023 | 7 | 1 |
| Hugo Larsson | ILL | 21 Aug 2023 | 28 Aug 2023 | 7 | 1 |
| Unknown player | Knock | 21 Aug 2023 | 1 Sept 2023 | 11 | 3 |
 Unknown player | ILL | 11 Aug 2023 | 21 Aug 2023 | 10 | 1 |
 Unknown player | Knee Surgery | 21 Jun 2023 | 19 Oct 2023 | 120 | 4 |
| Ansgar Knauff | Broken Collarbone | 17 Jun 2023 | 19 Aug 2023 | 63 | 5 |
| Unknown player | Shoulder Injury | 4 May 2023 | 12 May 2023 | 8 | 1 |
| Unknown player | Muscular Problems | 4 May 2023 | 7 May 2023 | 3 | 0 |
| Unknown player | Knee Injury | 3 May 2023 | 20 Jun 2023 | 48 | 6 |
 Randal Kolo Muani | Adductor Pain | 28 Apr 2023 | 2 May 2023 | 4 | 1 |
| Kristijan Jakic | Calf Injury | 16 Apr 2023 | 23 May 2023 | 37 | 6 |
 Evan Ndicka | Muscular Problems | 13 Apr 2023 | 1 May 2023 | 18 | 3 |
 Unknown player | Fitness | 12 Apr 2023 | 19 Apr 2023 | 7 | 1 |
 Unknown player | Hamstring Injury | 12 Apr 2023 | 23 May 2023 | 41 | 7 |
 Unknown player | Tear Of The Lateral Meniscus | 29 Mar 2023 | 30 Jun 2023 | 93 | 12 |
| Unknown player | Muscular Problems | 28 Mar 2023 | 11 Apr 2023 | 14 | 1 |
| Unknown player | Injury | 17 Mar 2023 | 20 Mar 2023 | 3 | — |
| Ansgar Knauff | Hip Problems | 10 Mar 2023 | 14 Mar 2023 | 4 | 1 |
 Unknown player | Ankle Injury | 8 Mar 2023 | 24 Apr 2023 | 47 | 9 |
| Unknown player | Cold | 3 Mar 2023 | 7 Mar 2023 | 4 | 1 |
| Mario Götze | Adductor Pain | 24 Feb 2023 | 1 Mar 2023 | 5 | 1 |
| Unknown player | ILL | 17 Feb 2023 | 20 Feb 2023 | 3 | 1 |
| Unknown player | Thigh Problems | 5 Feb 2023 | 11 Feb 2023 | 6 | 1 |
 Unknown player | Doubtful | 4 Feb 2023 | 4 Feb 2023 | 0 | 1 |
| Unknown player | Fitness | 31 Jan 2023 | 15 Feb 2023 | 15 | 3 |
| Kevin Trapp | Cold | 24 Jan 2023 | 27 Jan 2023 | 3 | 1 |
| Junior Dina Ebimbe | Syndesmotic Ligament Tear | 22 Jan 2023 | 20 Mar 2023 | 57 | 10 |
 Luca Pellegrini | Calf Injury | 20 Jan 2023 | 31 Jan 2023 | 11 | — |
| Unknown player | Injury | 18 Jan 2023 | 28 Feb 2023 | 41 | 9 |
| Unknown player | Ankle Injury | 13 Jan 2023 | 23 Jan 2023 | 10 | 3 |
| Unknown player | Metatarsal Fracture | 30 Nov 2022 | 30 Jan 2023 | 61 | 7 |
| Unknown player | Calf Problems | 7 Nov 2022 | 11 Nov 2022 | 4 | 1 |
| Timothy Chandler | Infection | 3 Nov 2022 | 7 Nov 2022 | 4 | 1 |
 Daichi Kamada | Infection | 3 Nov 2022 | 7 Nov 2022 | 4 | 1 |
 Unknown player | Hamstring Injury | 27 Oct 2022 | 15 Nov 2022 | 19 | 5 |
| Unknown player | Inner Knee Ligament Tear | 13 Oct 2022 | 31 Dec 2022 | 79 | 13 |
| Ansgar Knauff | Hamstring Injury | 10 Oct 2022 | 31 Oct 2022 | 21 | 6 |
| Luca Pellegrini | Shoulder Injury | 10 Oct 2022 | 17 Oct 2022 | 7 | 2 |
| Unknown player | Rest | 6 Oct 2022 | 10 Oct 2022 | 4 | 1 |
| Unknown player | Fitness | 6 Oct 2022 | 17 Oct 2022 | 11 | 3 |
| Mario Götze | Ankle Injury | 3 Oct 2022 | 6 Oct 2022 | 3 | 1 |
| Kristijan Jakic | Inflammation | 19 Sept 2022 | 3 Oct 2022 | 14 | 1 |
| Unknown player | Cold | 15 Sept 2022 | 22 Sept 2022 | 7 | 1 |
| Unknown player | Hamstring Injury | 8 Sept 2022 | 29 Sept 2022 | 21 | 3 |
 Unknown player | Adductor Injury | 8 Sept 2022 | 17 Oct 2022 | 39 | 8 |
| Luca Pellegrini | Thigh Problems | 8 Sept 2022 | 19 Sept 2022 | 11 | 3 |
| Unknown player | Hamstring Injury | 5 Sept 2022 | 12 Sept 2022 | 7 | 2 |
| Luca Pellegrini | Thigh Problems | 1 Sept 2022 | 5 Sept 2022 | 4 | 1 |
 Unknown player | Muscular Problems | 18 Aug 2022 | 1 Sept 2022 | 14 | — |
| Unknown player | Hamstring Injury | 15 Aug 2022 | 6 Oct 2022 | 52 | 9 |
| Unknown player | Hamstring Strain | 28 Jul 2022 | 25 Aug 2022 | 28 | 5 |
 Unknown player | Injury | 15 Jul 2022 | 1 Oct 2022 | 78 | 13 |
 Danny da Costa | Pubic Bone Irritation | 12 May 2022 | 16 May 2022 | 4 | 1 |
 Unknown player | Torn Muscle Fiber | 5 May 2022 | 30 Jun 2022 | 56 | 1 |
| Unknown player | Rest | 28 Apr 2022 | 5 May 2022 | 7 | 2 |
