| Season | Round | 1st Leg | 2nd Leg | Aggregate | |
| 2021/22 | Q1 | BIRKIRKARA vs La Fiorita 1967 (SMR) | 1-0 | 1-1 | (2-1) |
| Q1 | UE Sant Julià (AND) vs GZIRA UNITED | 0-0 | 1-1 | (1-1)(3-5 pen) | |
| Q1 | Mosta vs FK Spartak Trnava (SVK) | 3-2 | 0-2 | (3-4) | |
| Q2 | SS Folgore (SMR) vs HIBERNIANS | 1-3 | 2-4 | (3-7) | |
| Q2 | Olimpija Ljubljana (SLO) vs Birkirkara | 1-0 | 0-1 | (1-1)(5-4 pen) | |
| Q2 | Gzira United vs HNK Rijeka (CRO) | 0-2 | 0-1 | (0-3) | |
| Q3 | Riga FC (LAT) vs Hibernians | 0-1 | 4-1 aet | (4-2) | |
| 2022/23 | Q1 | GZIRA UNITED vs Atletic Club d’Escaldes (AND) | 1-1 | 1-0 | (2-1) |
| Q1 | FC Alashkert (ARM) vs HAMRUN SPARTANS | 1-0 | 1-4 | (2-4) | |
| Q1 | Floriana vs Petrocub-Hincesti (MOL) | 0-0 | 0-1 | (0-1) | |
| Q2 | HIBERNIANS vs FCI Levadia Tallinn (EST) | 3-2 | 1-1 | (4-3) | |
| Q2 | GZIRA UNITED vs FK Radnicki Nis (SRB) | 2-2 | 3-3 aet | (5-5)(3-1 pen) | |
| Q2 | FK Velez Mostar (BIH) vs HAMRUN SPARTANS | 0-1 | 0-1 | (0-2) | |
| Q3 | RFS (LAT) vs Hibernians | 1-1 | 3-1 | (4-2) | |
| Q3 | HAMRUN SPARTANS vs Levski Sofia (BUL) | 0-1 | 2-1 aet | (2-2)(4-1 pen) | |
| Q3 | Wolfsberger (AUT) vs Gzira United | 0-0 | 4-0 | (4-0) | |
| PO | FK Partizan (SRB) vs Hamrun Spartans | 4-1 | 3-3 | (7-4) | |
| 2023/24 | Q1 | NK Domzale (SLO) vs BALZAN | 1-4 | 3-1 aet | (4-5) |
| Q1 | NK Maribor (SLO) vs Birkirkara | 1-1 | 2-1 | (3-2) | |
| Q1 | GZIRA UNITED vs Glentoran (NIR) | 2-2 | 1-1 aet | (3-3)(14-13 pen) | |
| Q2 | HAMRUN SPARTANS vs Dinamo Tbilisi (GEO) | 2-1 | 1-0 | (3-1) | |
| Q2 | Neman Grodno (BLR) vs Balzan | 2-0 | 0-0 | (2-0) | |
| Q2 | GZIRA UNITED vs F91 Diddeleng (LUX) | 2-0 | 1-2 | (3-2) | |
| Q3 | Hamrun Spartans vs Ferencváros (HUN) | 1-6 | 1-2 | (2-8) | |
| Q3 | Viktoria Plzeň (CZE) vs Gzira United | 4-0 | 2-0 | (6-0) | |
| 2024/25 | Q1 | FLORIANA vs SP Tre Penne (SMR) | 3-1 | 1-1 | (4-2) |
| Q1 | FK Partizani Tirana (ALB) vs Marsaxlokk | 1-1 | 2-1 | (3-2) | |
| Q2 | FC Noah (ARM) vs Sliema Wanderers | 7-0 | 0-0 | (7-0) | |
| Q2 | Floriana vs SC Victoria (POR) | 0-1 | 0-4 | (0-5) | |
| Q2 | FC Ballkani (KOS) vs Hamrun Spartans | 0-0 | 2-0 | (2-0) | |
| 2025/26 | Q1 | FLORIANA vs Haverfordwest County (WAL) | 2-1 | 3-2 | (5-3) |
| Q1 | Birkirkara vs FC Petrocub (MOL) | 1-0 | 0-3 | (1-3) | |
| Q2 | Hibernians vs FC Spartak Trnava (SVK) | 1-2 | 1-5 | (2-7) | |
| Q2 | FC Ballkani (KOS) vs Floriana | 4-2 | 1-1 | (5-3) | |
| PO | HAMRUN SPARTANS vs FK RFS (LAT) | 1-0 | 2-2 | (3-2) | |
| LS | Jagiellonia Białystok (POL) vs Hamrun Spartans | ||||
| LS | Hamrun Spartans vs Lausanne Sport (SUI) | ||||
| LS | Samsunspor (TUR) vs Hamrun Spartans | ||||
| LS | Hamrun Spartans vs Lincoln Red Imps (GIB) | ||||
| LS | Hamrun Spartans vs FC Shakhtar (UKR) | ||||
| LS | Shamrock Rovers (IRL) vs Hamrun Spartans |
Notes:-
- Names of local clubs in uppercase indicate that the club moved to the next round.
- Teams eliminated from the UEFA Champions League preliminary and first qualifying round, enter the UEFA Europa Conference League.
- As from 2021/22, the away-goals rule has been abolished.
- The competition, originally known as UEFA Europa Conference League had its name changed to UEFA Conference League as from season 2024/25.