| Player | Reason | From | Until | Days | Games missed |
|---|---|---|---|---|---|
 Farès Chaïbi | Infection | 11 Sept 2026 | Current | — | 1 |
 Oscar Højlund | Hip Problems | 11 Sept 2026 | Current | — | 1 |
 Ansgar Knauff | Hamstring Injury | 27 Aug 2026 | Current | — | 3 |
 Ritsu Doan | Muscular Problems | 19 Aug 2026 | 1 Sept 2026 | 13 | 2 |
 Hugo Larsson | Muscular Problems | 15 Aug 2026 | 30 Aug 2026 | 15 | 3 |
 Timothy Chandler | Hamstring Injury | 8 Aug 2026 | 25 Aug 2026 | 17 | 4 |
 Jessic Ngankam | Hamstring Injury | 7 Aug 2026 | — | — | 7 |
 Nnamdi Collins | Back Problems | 4 Aug 2026 | 7 Sept 2026 | 34 | 6 |
 Noël Aséko | Knee Problems | 31 Jul 2026 | 26 Aug 2026 | 26 | 5 |
| Oscar Højlund | Knock | 15 May 2026 | 17 May 2026 | 2 | 1 |
 Jens Grahl | Fitness | 6 May 2026 | 11 May 2026 | 5 | 1 |
| Jens Grahl | Hamstring Injury | 21 Apr 2026 | 5 May 2026 | 14 | 2 |
 Jean-Mattéo Bahoya | Fitness | 14 Apr 2026 | 27 Apr 2026 | 13 | 2 |
 Unknown player | Torn Muscle Fiber | 9 Apr 2026 | 11 Jun 2026 | 63 | 8 |
| Ritsu Doan | ILL | 9 Apr 2026 | 17 Apr 2026 | 8 | 1 |
| Jean-Mattéo Bahoya | Hamstring Injury | 22 Mar 2026 | 13 Apr 2026 | 22 | 2 |
| Nnamdi Collins | Ankle Injury | 22 Mar 2026 | 30 Jun 2026 | 100 | 10 |
 Unknown player | Fitness | 6 Mar 2026 | 4 May 2026 | 59 | 8 |
 Can Uzun | Fitness | 6 Mar 2026 | 16 Mar 2026 | 10 | 2 |
 Kauã Santos | Inner Knee Ligament Tear | 2 Mar 2026 | 28 Apr 2026 | 57 | 7 |
 Robin Koch | ILL | 19 Feb 2026 | 25 Feb 2026 | 6 | 1 |
| Ansgar Knauff | Surgery | 17 Feb 2026 | 16 Mar 2026 | 27 | 4 |
 Unknown player | Ankle Injury | 15 Feb 2026 | 24 Apr 2026 | 68 | 8 |
| Farès Chaïbi | Knee Problems | 12 Feb 2026 | 18 Feb 2026 | 6 | 1 |
 Arthur Theate | Meniscus Injury | 11 Feb 2026 | 18 Mar 2026 | 35 | 5 |
 Jonathan Burkardt | ILL | 10 Feb 2026 | 15 Feb 2026 | 5 | 0 |
| Ansgar Knauff | Cold | 5 Feb 2026 | 10 Feb 2026 | 5 | 1 |
| Jonathan Burkardt | Fitness | 2 Feb 2026 | 8 Feb 2026 | 6 | 1 |
| Nnamdi Collins | Knee Problems | 30 Jan 2026 | 2 Feb 2026 | 3 | 1 |
| Can Uzun | Hamstring Injury | 25 Jan 2026 | 6 Mar 2026 | 40 | 6 |
 Mario Götze | ILL | 15 Jan 2026 | 19 Jan 2026 | 4 | 1 |
 Younes Ebnoutalib | Inner Knee Ligament Tear | 13 Jan 2026 | 18 Mar 2026 | 64 | 12 |
| Hugo Larsson | ILL | 12 Jan 2026 | 19 Jan 2026 | 7 | 2 |
| Farès Chaïbi | Rest | 12 Jan 2026 | 14 Jan 2026 | 2 | 0 |
 Nathaniel Brown | ILL | 12 Jan 2026 | 14 Jan 2026 | 2 | 1 |
| Can Uzun | Foot Injury | 12 Jan 2026 | 14 Jan 2026 | 2 | 0 |
 Ellyes Skhiri | Rest | 9 Jan 2026 | 10 Jan 2026 | 1 | 1 |
| Jean-Mattéo Bahoya | ILL | 5 Jan 2026 | 12 Jan 2026 | 7 | 1 |
 Elias Baum | Inner Ligament Injury | 20 Dec 2025 | 11 Feb 2026 | 53 | 9 |
| Mario Götze | ILL | 20 Dec 2025 | 22 Dec 2025 | 2 | 1 |
 Elye Wahi | ILL | 17 Dec 2025 | 22 Dec 2025 | 5 | 1 |
| Hugo Larsson | Knock | 13 Dec 2025 | 17 Dec 2025 | 4 | 1 |
 Unknown player | Adductor Pain | 12 Dec 2025 | 14 Dec 2025 | 2 | — |
| Timothy Chandler | Ankle Problems | 8 Dec 2025 | 26 Jan 2026 | 49 | 8 |
| Unknown player | Foot Injury | 7 Dec 2025 | 5 Mar 2026 | 88 | 14 |
| Ansgar Knauff | ILL | 6 Dec 2025 | 8 Dec 2025 | 2 | 1 |
| Jonathan Burkardt | Calf Injury | 27 Nov 2025 | 1 Feb 2026 | 66 | 5 |
| Hugo Larsson | Muscle Injury | 12 Nov 2025 | 4 Dec 2025 | 22 | 3 |
| Can Uzun | Muscle Injury | 2 Nov 2025 | 4 Dec 2025 | 32 | 4 |
 Unknown player | Injury | 31 Oct 2025 | 28 Nov 2025 | 28 | 3 |
| Oscar Højlund | Muscle Injury | 21 Oct 2025 | 24 Nov 2025 | 34 | 7 |
| Jessic Ngankam | Fitness | 16 Oct 2025 | 16 Nov 2025 | 31 | 7 |
| Elias Baum | Hamstring Injury | 9 Oct 2025 | 9 Nov 2025 | 31 | 6 |
| Elias Baum | ILL | 3 Oct 2025 | 6 Oct 2025 | 3 | 1 |
| Unknown player | Muscle Injury | 13 Sept 2025 | 10 Oct 2025 | 27 | 5 |
| Hugo Larsson | Stomach Flu | 12 Sept 2025 | 15 Sept 2025 | 3 | 1 |
| Mario Götze | Muscular Problems | 30 Aug 2025 | 19 Sept 2025 | 20 | 2 |
| Jonathan Burkardt | Back Problems | 30 Aug 2025 | 9 Sept 2025 | 10 | 1 |
| Elias Baum | Fitness | 16 Aug 2025 | 24 Aug 2025 | 8 | 1 |
| Kauã Santos | Fitness | 15 Aug 2025 | 1 Sept 2025 | 17 | 3 |
| Ellyes Skhiri | Knee Problems | 22 Jul 2025 | 25 Aug 2025 | 34 | 5 |
| Jean-Mattéo Bahoya | Ankle Problems | 17 May 2025 | 21 May 2025 | 4 | 1 |
 Unknown player | Muscular Problems | 11 May 2025 | 30 Jun 2025 | 50 | 3 |
| Unknown player | Muscular Problems | 26 Apr 2025 | 30 Apr 2025 | 4 | 1 |
 Igor Matanovic | ILL | 23 Apr 2025 | 30 Apr 2025 | 7 | 1 |
| Mario Götze | Torn Muscle Fiber | 18 Apr 2025 | 18 Jun 2025 | 61 | 6 |
| Kauã Santos | Cruciate Ligament Tear | 18 Apr 2025 | 14 Aug 2025 | 118 | 10 |
| Can Uzun | Infection | 30 Mar 2025 | 7 Apr 2025 | 8 | 1 |
| Ansgar Knauff | Knee Injury | 29 Mar 2025 | 14 Apr 2025 | 16 | 3 |
| Igor Matanovic | Fitness | 26 Mar 2025 | 31 Mar 2025 | 5 | 1 |
 Junior Dina Ebimbe | Stomach Flu | 19 Mar 2025 | 7 Apr 2025 | 19 | 3 |
| Elye Wahi | Knee Injury | 15 Mar 2025 | 7 Apr 2025 | 23 | 4 |
 Kevin Trapp | Shin Injury | 12 Mar 2025 | 18 Apr 2025 | 37 | 7 |
 Aurèle Amenda | Calf Injury | 9 Mar 2025 | 12 Mar 2025 | 3 | 1 |
| Arthur Theate | Muscle Injury | 9 Mar 2025 | 27 Mar 2025 | 18 | 4 |
| Robin Koch | Infection | 8 Mar 2025 | 11 Mar 2025 | 3 | 1 |
| Robin Koch | Concussion | 2 Mar 2025 | 7 Mar 2025 | 5 | 0 |
| Timothy Chandler | Hamstring Injury | 27 Feb 2025 | 7 Apr 2025 | 39 | 8 |
 Unknown player | Knee Injury | 19 Feb 2025 | 30 Jun 2025 | 131 | 14 |
| Junior Dina Ebimbe | Fitness | 12 Feb 2025 | 8 Mar 2025 | 24 | 4 |
| Ellyes Skhiri | Knock | 8 Feb 2025 | 19 Feb 2025 | 11 | 2 |
| Robin Koch | Shoulder Injury | 3 Feb 2025 | 24 Feb 2025 | 21 | 2 |
| Igor Matanovic | Foot Injury | 1 Feb 2025 | 25 Mar 2025 | 52 | 10 |
 Unknown player | Muscular Problems | 30 Jan 2025 | 22 Oct 2025 | 265 | 36 |
| Elye Wahi | Fitness | 27 Jan 2025 | 7 Feb 2025 | 11 | 2 |
| Nathaniel Brown | ILL | 24 Jan 2025 | 1 Feb 2025 | 8 | 2 |
 Unknown player | Cold | 22 Jan 2025 | 28 Jan 2025 | 6 | 2 |
| Oscar Højlund | Cold | 22 Jan 2025 | 28 Jan 2025 | 6 | 2 |
| Junior Dina Ebimbe | Calf Injury | 21 Jan 2025 | 11 Feb 2025 | 21 | 5 |
| Jean-Mattéo Bahoya | Broken Nose Bone | 5 Jan 2025 | 13 Jan 2025 | 8 | 1 |
| Kevin Trapp | ILL | 20 Dec 2024 | 25 Dec 2024 | 5 | 1 |
| Unknown player | Calf Problems | 13 Dec 2024 | 7 Jan 2025 | 25 | 2 |
| Junior Dina Ebimbe | Cold | 11 Dec 2024 | 16 Dec 2024 | 5 | 1 |
| Hugo Larsson | Muscular Problems | 6 Dec 2024 | 13 Dec 2024 | 7 | 1 |
| Arthur Theate | Torn Lateral Ankle Ligament | 1 Dec 2024 | 6 Dec 2024 | 5 | 2 |
| Unknown player | ILL | 19 Nov 2024 | 25 Nov 2024 | 6 | 1 |
| Aurèle Amenda | Syndesmosis Ligament Tear | 17 Nov 2024 | 25 Jan 2025 | 69 | 12 |
| Oscar Højlund | Fitness | 13 Nov 2024 | 29 Nov 2024 | 16 | 1 |
| Unknown player | Hamstring Injury | 28 Oct 2024 | 24 Nov 2024 | 27 | 4 |
 Niels Nkounkou | Allergic Reaction | 25 Oct 2024 | 29 Oct 2024 | 4 | 1 |
