| Round of 16 — Direct Qualification | ||||||||||
| 1 | West Ham | 6 | 5 | 1 | 0 | 20 | 6 | +14 | 16 | Direct |
| 2 | RFS | 6 | 5 | 1 | 0 | 17 | 7 | +10 | 16 | Direct |
| 3 | Aston Villa | 6 | 5 | 0 | 1 | 16 | 5 | +11 | 15 | Direct |
| 4 | Elbasani | 6 | 4 | 1 | 1 | 20 | 10 | +10 | 13 | Direct |
| 5 | Panathinaikos 2 | 6 | 4 | 0 | 2 | 16 | 10 | +6 | 12 | Direct |
| 6 | Longford Town | 6 | 4 | 0 | 2 | 11 | 6 | +5 | 12 | Direct |
| 7 | Basel | 6 | 4 | 0 | 2 | 11 | 8 | +3 | 12 | Direct |
| 8 | Metta LU | 6 | 4 | 0 | 2 | 16 | 16 | 0 | 12 | Direct |
| Knockout Playoff Round | ||||||||||
| 9 | Paide | 6 | 3 | 2 | 1 | 19 | 8 | +11 | 11 | Playoff |
| 10 | Real Sociedad 2 | 6 | 3 | 1 | 2 | 13 | 9 | +4 | 10 | Playoff |
| 11 | Sligo Rovers | 6 | 3 | 1 | 2 | 16 | 15 | +1 | 10 | Playoff |
| 12 | FC Andorra | 6 | 3 | 1 | 2 | 12 | 11 | +1 | 10 | Playoff |
| 13 | Anderlecht 2 | 6 | 3 | 1 | 2 | 11 | 10 | +1 | 10 | Playoff |
| 14 | Lyon 2 | 6 | 3 | 1 | 2 | 6 | 5 | +1 | 10 | Playoff |
| 15 | Coleraine | 6 | 3 | 1 | 2 | 9 | 9 | 0 | 10 | Playoff |
| 16 | Gent 2 | 6 | 3 | 1 | 2 | 14 | 15 | -1 | 10 | Playoff |
| 17 | Kayserispor | 6 | 3 | 1 | 2 | 9 | 10 | -1 | 10 | Playoff |
| 18 | FK Liepaja | 6 | 2 | 3 | 1 | 17 | 12 | +5 | 9 | Playoff |
| 19 | Sivasspor | 6 | 3 | 0 | 3 | 14 | 12 | +2 | 9 | Playoff |
| 20 | Rennes 2 | 6 | 3 | 0 | 3 | 12 | 15 | -3 | 9 | Playoff |
| 21 | Ludogorets | 6 | 2 | 2 | 2 | 11 | 10 | +1 | 8 | Playoff |
| 22 | Lech Poznan | 6 | 2 | 1 | 3 | 10 | 10 | 0 | 7 | Playoff |
| 23 | Midtjylland | 6 | 2 | 1 | 3 | 13 | 14 | -1 | 7 | Playoff |
| 24 | Lazio 2 | 6 | 2 | 1 | 3 | 9 | 14 | -5 | 7 | Playoff |
| Eliminated | ||||||||||
| 25 | Qarabag | 6 | 2 | 0 | 4 | 7 | 9 | -2 | 6 | Out |
| 26 | PAOK 2 | 6 | 1 | 3 | 2 | 13 | 17 | -4 | 6 | Out |
| 27 | Zrinjski | 6 | 2 | 0 | 4 | 8 | 12 | -4 | 6 | Out |
| 28 | Real Betis 2 | 6 | 1 | 3 | 2 | 6 | 13 | -7 | 6 | Out |
| 29 | Fiorentina 2 | 6 | 1 | 2 | 3 | 13 | 18 | -5 | 5 | Out |
| 30 | Jagiellonia Bialystok | 6 | 1 | 1 | 4 | 6 | 10 | -4 | 4 | Out |
| 31 | Rigas FS | 6 | 1 | 1 | 4 | 9 | 15 | -6 | 4 | Out |
| 32 | Vojvodina | 6 | 1 | 1 | 4 | 7 | 13 | -6 | 4 | Out |
| 33 | Narva Trans | 6 | 1 | 1 | 4 | 4 | 11 | -7 | 4 | Out |
| 34 | F91 Dudelange | 6 | 0 | 2 | 4 | 6 | 11 | -5 | 2 | Out |
| 35 | Glenavon | 6 | 0 | 2 | 4 | 5 | 17 | -12 | 2 | Out |
| 36 | Slovan Bratislava | 6 | 0 | 1 | 5 | 4 | 17 | -13 | 1 | Out |