| Round of 16 — Direct Qualification | ||||||||||
| 1 | West Ham | 6 | 5 | 1 | 0 | 16 | 5 | +11 | 16 | Direct |
| 2 | Aston Villa | 6 | 5 | 1 | 0 | 11 | 0 | +11 | 16 | Direct |
| 3 | Lech Poznan | 6 | 4 | 1 | 1 | 11 | 6 | +5 | 13 | Direct |
| 4 | Bohemian | 6 | 4 | 1 | 1 | 16 | 12 | +4 | 13 | Direct |
| 5 | Metta LU | 6 | 4 | 1 | 1 | 14 | 13 | +1 | 13 | Direct |
| 6 | Sheriff | 6 | 4 | 0 | 2 | 16 | 9 | +7 | 12 | Direct |
| 7 | Utrecht | 6 | 3 | 3 | 0 | 17 | 11 | +6 | 12 | Direct |
| 8 | Motherwell | 6 | 4 | 0 | 2 | 13 | 7 | +6 | 12 | Direct |
| Knockout Playoff Round | ||||||||||
| 9 | Cercle Brugge | 6 | 4 | 0 | 2 | 13 | 9 | +4 | 12 | Playoff |
| 10 | Lazio 2 | 6 | 3 | 2 | 1 | 18 | 13 | +5 | 11 | Playoff |
| 11 | Neftchi | 6 | 3 | 2 | 1 | 14 | 11 | +3 | 11 | Playoff |
| 12 | Gent 2 | 6 | 3 | 1 | 2 | 13 | 9 | +4 | 10 | Playoff |
| 13 | Panathinaikos 2 | 6 | 3 | 1 | 2 | 10 | 11 | -1 | 10 | Playoff |
| 14 | Real Sociedad 2 | 6 | 3 | 1 | 2 | 13 | 16 | -3 | 10 | Playoff |
| 15 | Trans | 6 | 2 | 3 | 1 | 6 | 7 | -1 | 9 | Playoff |
| 16 | Hajduk Split | 6 | 3 | 0 | 3 | 12 | 14 | -2 | 9 | Playoff |
| 17 | Kukes | 6 | 2 | 2 | 2 | 14 | 15 | -1 | 8 | Playoff |
| 18 | Elbasani | 6 | 2 | 1 | 3 | 16 | 14 | +2 | 7 | Playoff |
| 19 | Zalgiris Vilnius | 6 | 2 | 1 | 3 | 10 | 8 | +2 | 7 | Playoff |
| 20 | Petrocub | 6 | 2 | 1 | 3 | 12 | 11 | +1 | 7 | Playoff |
| 21 | HJK | 6 | 2 | 1 | 3 | 11 | 12 | -1 | 7 | Playoff |
| 22 | Anderlecht 2 | 6 | 2 | 1 | 3 | 10 | 11 | -1 | 7 | Playoff |
| 23 | Lyon 2 | 6 | 2 | 1 | 3 | 10 | 11 | -1 | 7 | Playoff |
| 24 | Jagiellonia Bialystok | 6 | 2 | 1 | 3 | 9 | 10 | -1 | 7 | Playoff |
| Eliminated | ||||||||||
| 25 | Rennes 2 | 6 | 2 | 1 | 3 | 7 | 10 | -3 | 7 | Out |
| 26 | Real Betis 2 | 6 | 1 | 3 | 2 | 12 | 14 | -2 | 6 | Out |
| 27 | Fiorentina 2 | 6 | 1 | 3 | 2 | 10 | 13 | -3 | 6 | Out |
| 28 | Rosenborg | 6 | 1 | 3 | 2 | 7 | 12 | -5 | 6 | Out |
| 29 | Narva Trans | 6 | 1 | 2 | 3 | 8 | 10 | -2 | 5 | Out |
| 30 | Teuta | 6 | 1 | 2 | 3 | 6 | 9 | -3 | 5 | Out |
| 31 | KR Reykjavik | 6 | 1 | 1 | 4 | 7 | 11 | -4 | 4 | Out |
| 32 | PAOK 2 | 6 | 1 | 1 | 4 | 12 | 19 | -7 | 4 | Out |
| 33 | FK Liepaja | 6 | 0 | 3 | 3 | 5 | 12 | -7 | 3 | Out |
| 34 | Kayserispor | 6 | 1 | 0 | 5 | 6 | 16 | -10 | 3 | Out |
| 35 | Sivasspor | 6 | 0 | 2 | 4 | 4 | 10 | -6 | 2 | Out |
| 36 | Europa FC | 6 | 0 | 2 | 4 | 6 | 14 | -8 | 2 | Out |