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| | | Draw Tuesday, 17th June 2025 |
| dates | team 1 | Leg 1 | Leg 2 | team 2 | HT1 | HT2 | aggr. | | Group 1 | | 09.07, 15.07 | Žalgiris Vilnius |  LTU | 2-0 | --- | Ħamrun Spartans |  MLT | | | | | 08.07, 15.07 | KuPS Kuopio |  FIN | 1-0 | --- | Milsami Orhei |  MDA | | | | | 08.07, 15.07 | The New Saints |  WAL | 0-0 | --- | Shkëndija |  MKD | | | | | 08.07, 15.07 | Iberia 1999 |  GEO | 1-3 | --- | Malmö FF |  SWE | | | | | 08.07, 15.07 | Levadia Tallinn |  EST | 0-1 | --- | RFS |  LAT | | | | | Group 2 | | 08.07, 15.07 | Drita |  KOS | 1-0 | --- | Differdange |  LUX | | | | | 08.07, 15.07 | Víkingur |  FAR | 2-3 | --- | Lincoln Red Imps |  GIB | | | | | 08.07, 15.07 | KF Egnatia |  ALB | 1-0 | --- | Breiðablik |  ISL | | | | | 09.07, 15.07 | Shelbourne |  IRL | 1-0 | --- | Linfield FK |  NIR | | | | | 09.07, 15.07 | Football Club FCSB |  ROU | 3-1 | --- | Inter Club d'Escaldes |  AND | | | | | Group 3 | | 08.07, 15.07 | Virtus AC 1964 |  SMR | 0-2 | --- | Zrinjski Mostar |  BIH | | | | | 08.07, 15.07 | Olimpija Ljubljana |  SLO | 1-1 | --- | Kairat Alma-Aty |  KAZ | | | | | 08.07, 15.07 | Noah |  ARM | 1-0 | --- | Budućnost Podgorica |  MNE | | | | | 09.07, 15.07 | Ludogorets Razgrad |  BUL | 1-0 | --- | Dinamo Minsk |  BLR | | | | |
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