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| 1st(1st leg) | FK AP Brera Strumica | - | FK Sarajevo Academy | 2:2 (0:1) | ||
| 2nd (2nd leg) | FK Sarajevo Academy | - | FK AP Brera Strumica | 2:0 (0:0) | ||
| 1st(1st leg): 17/09/2024 14:00 | 2nd (2nd leg): 02/10/2024 17:00 | Winner: FK Sarajevo Academy | ||||
| 1st(1st leg) | FK Kairat | - | Academia Rebeja Chisinau | 2:1 (1:0) | ||
| 2nd (2nd leg) | Academia Rebeja Chisinau | - | FK Kairat | 1:4 (0:2) | ||
| 1st(1st leg): 18/09/2024 12:00 | 2nd (2nd leg): 02/10/2024 13:00 | Winner: FK Kairat | ||||
| 1st(1st leg) | KF Bylis Ballsh | - | KF 2 Korriku | 1:2 (0:0) | ||
| 2nd (2nd leg) | KF 2 Korriku | - | KF Bylis Ballsh | 2:1 (0:0) | ||
| 1st(1st leg): 18/09/2024 15:00 | 2nd (2nd leg): 02/10/2024 13:00 | Winner: KF 2 Korriku | ||||
| 1st(1st leg) | BFC Daugavpils | - | Cliftonville FC | 1:0 (1:0) | ||
| 2nd (2nd leg) | Cliftonville FC | - | BFC Daugavpils | 2:4 (1:0, 2:1) pso | ||
| 1st(1st leg): 18/09/2024 16:00 | 2nd (2nd leg): 02/10/2024 19:30 | Winner: BFC Daugavpils | ||||
| 1st(1st leg) | Dinamo Tbilisi | - | FK Budućnost Podgorica | 3:2 (1:2) | ||
| 2nd (2nd leg) | FK Budućnost Podgorica | - | Dinamo Tbilisi | 4:1 (2:1) | ||
| 1st(1st leg): 18/09/2024 16:00 | 2nd (2nd leg): 02/10/2024 18:00 | Winner: FK Budućnost Podgorica | ||||
| 1st(1st leg) | FC Honka | - | Valletta FC | 1:0 (0:0) | ||
| 2nd (2nd leg) | Valletta FC | - | FC Honka | 3:0 (0:1, 3:2) pso | ||
| 1st(1st leg): 18/09/2024 16:30 | 2nd (2nd leg): 02/10/2024 18:00 | Winner: Valletta FC | ||||
| 1st(1st leg) | FK Žalgiris | - | The New Saints | 3:2 (1:2) | ||
| 2nd (2nd leg) | The New Saints | - | FK Žalgiris | 0:4 (0:2) | ||
| 1st(1st leg): 18/09/2024 17:00 | 2nd (2nd leg): 01/10/2024 19:00 | Winner: FK Žalgiris | ||||
| 1st(1st leg) | Dinamo Minsk | - | Pyunik FC | 4:2 (2:0) | ||
| 2nd (2nd leg) | Pyunik FC | - | Dinamo Minsk | 1:2 (0:2) | ||
| 1st(1st leg): 18/09/2024 17:00 | 2nd (2nd leg): 22/09/2024 17:00 | Winner: Dinamo Minsk | ||||
| 1st(1st leg) | Lincoln Red Imps | - | NK Maribor | 0:6 (0:2) | ||
| 2nd (2nd leg) | NK Maribor | - | Lincoln Red Imps | 2:0 (1:0) | ||
| 1st(1st leg): 18/09/2024 17:30 | 2nd (2nd leg): 02/10/2024 16:00 | Winner: NK Maribor | ||||
| 1st(1st leg) | JK Tallinna Kalev | - | FC Santa Coloma | 7:0 (3:0) | ||
| 2nd (2nd leg) | FC Santa Coloma | - | JK Tallinna Kalev | 0:4 (0:1) | ||
| 1st(1st leg): 18/09/2024 17:30 | 2nd (2nd leg): 02/10/2024 18:30 | Winner: JK Tallinna Kalev | ||||
| 1st(1st leg) | HB Tórshavn | - | Progrès Niedercorn | 1:2 (0:1) | ||
| 2nd (2nd leg) | Progrès Niedercorn | - | HB Tórshavn | 3:0 (2:0) | ||
| 1st(1st leg): 18/09/2024 19:00 | 2nd (2nd leg): 02/10/2024 18:00 | Winner: Progrès Niedercorn | ||||
| 1st(1st leg) | UC Dublin | - | UMF Stjarnan | 3:0 (1:0) | ||
| 2nd (2nd leg) | UMF Stjarnan | - | UC Dublin | 3:2 (1:1) | ||
| 1st(1st leg): 18/09/2024 19:30 | 2nd (2nd leg): 02/10/2024 20:00 | Winner: UC Dublin | ||||
