| Round of 16 — Direct Qualification | ||||||||||
| 1 | Aston Villa | 6 | 6 | 0 | 0 | 21 | 1 | +20 | 18 | Direct |
| 2 | West Ham | 6 | 6 | 0 | 0 | 20 | 2 | +18 | 18 | Direct |
| 3 | Lyon 2 | 6 | 6 | 0 | 0 | 23 | 8 | +15 | 18 | Direct |
| 4 | Jagiellonia Bialystok | 6 | 4 | 1 | 1 | 14 | 7 | +7 | 13 | Direct |
| 5 | Real Sociedad 2 | 6 | 4 | 1 | 1 | 15 | 15 | 0 | 13 | Direct |
| 6 | RFS | 6 | 3 | 3 | 0 | 14 | 6 | +8 | 12 | Direct |
| 7 | Levadia Tallinn | 6 | 3 | 3 | 0 | 10 | 6 | +4 | 12 | Direct |
| 8 | Riga FC | 6 | 3 | 2 | 1 | 12 | 8 | +4 | 11 | Direct |
| Knockout Playoff Round | ||||||||||
| 9 | Tre Fiori | 6 | 3 | 1 | 2 | 15 | 9 | +6 | 10 | Playoff |
| 10 | FC Santa Coloma | 6 | 3 | 1 | 2 | 14 | 9 | +5 | 10 | Playoff |
| 11 | PAOK 2 | 6 | 3 | 1 | 2 | 12 | 10 | +2 | 10 | Playoff |
| 12 | Lech Poznan | 6 | 3 | 1 | 2 | 12 | 11 | +1 | 10 | Playoff |
| 13 | Red Star | 6 | 3 | 1 | 2 | 10 | 9 | +1 | 10 | Playoff |
| 14 | Rennes 2 | 6 | 3 | 1 | 2 | 10 | 10 | 0 | 10 | Playoff |
| 15 | Kayserispor | 6 | 2 | 3 | 1 | 12 | 7 | +5 | 9 | Playoff |
| 16 | Zrinjski | 6 | 3 | 0 | 3 | 15 | 14 | +1 | 9 | Playoff |
| 17 | Sivasspor | 6 | 3 | 0 | 3 | 14 | 18 | -4 | 9 | Playoff |
| 18 | Gent | 6 | 2 | 2 | 2 | 11 | 9 | +2 | 8 | Playoff |
| 19 | Molde | 6 | 2 | 2 | 2 | 10 | 13 | -3 | 8 | Playoff |
| 20 | Panathinaikos 2 | 6 | 2 | 1 | 3 | 16 | 15 | +1 | 7 | Playoff |
| 21 | Gent 2 | 6 | 2 | 1 | 3 | 14 | 13 | +1 | 7 | Playoff |
| 22 | Real Betis 2 | 6 | 2 | 1 | 3 | 13 | 16 | -3 | 7 | Playoff |
| 23 | Elbasani | 6 | 2 | 1 | 3 | 8 | 11 | -3 | 7 | Playoff |
| 24 | Glentoran | 6 | 2 | 1 | 3 | 6 | 14 | -8 | 7 | Playoff |
| Eliminated | ||||||||||
| 25 | Anderlecht 2 | 6 | 2 | 0 | 4 | 12 | 9 | +3 | 6 | Out |
| 26 | Trans | 6 | 2 | 0 | 4 | 10 | 14 | -4 | 6 | Out |
| 27 | Sliema Wanderers | 6 | 2 | 0 | 4 | 9 | 13 | -4 | 6 | Out |
| 28 | Fiorentina 2 | 6 | 2 | 0 | 4 | 11 | 17 | -6 | 6 | Out |
| 29 | Utrecht | 6 | 2 | 0 | 4 | 7 | 13 | -6 | 6 | Out |
| 30 | Tirana | 6 | 2 | 0 | 4 | 10 | 17 | -7 | 6 | Out |
| 31 | Wisla Krakow | 6 | 1 | 3 | 2 | 10 | 21 | -11 | 6 | Out |
| 32 | Lazio 2 | 6 | 1 | 2 | 3 | 11 | 19 | -8 | 5 | Out |
| 33 | FK Zalgiris | 6 | 1 | 0 | 5 | 6 | 13 | -7 | 3 | Out |
| 34 | Floriana | 6 | 1 | 0 | 5 | 4 | 16 | -12 | 3 | Out |
| 35 | Besiktas | 6 | 0 | 1 | 5 | 6 | 15 | -9 | 1 | Out |
| 36 | Hearts | 6 | 0 | 0 | 6 | 3 | 12 | -9 | 0 | Out |