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| | | Draw Tuesday, 17th June 2025 |
| Group 1 | | 08.07, 15.07 | Žalgiris Vilnius |  LTU | Ħamrun Spartans |  MLT | | 08.07, 15.07 | KuPS Kuopio |  FIN | Milsami Orhei |  MDA | | 08.07, 15.07 | The New Saints |  WAL | Shkëndija |  MKD | | 08.07, 15.07 | Iberia 1999 |  GEO | Malmö FF |  SWE | | 08.07, 15.07 | Levadia Tallinn |  EST | RFS |  LAT | | Group 2 | | 08.07, 15.07 | Drita |  KOS | Differdange |  LUX | | 08.07, 15.07 | Víkingur |  FAR | Lincoln Red Imps |  GIB | | 08.07, 15.07 | KF Egnatia |  ALB | Breiðablik |  ISL | | 08.07, 15.07 | Shelbourne |  IRL | Linfield FK |  NIR | | 08.07, 15.07 | Football Club FCSB |  ROU | Inter Club d'Escaldes |  AND | | Group 3 | | 08.07, 15.07 | Virtus AC 1964 |  SMR | Zrinjski Mostar |  BIH | | 08.07, 15.07 | Olimpija Ljubljana |  SLO | Kairat Alma-Aty |  KAZ | | 08.07, 15.07 | Noah |  ARM | Budućnost Podgorica |  MNE | | 08.07, 15.07 | Ludogorets Razgrad |  BUL | Dinamo Minsk |  BLR | |
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