| Round of 16 — Direct Qualification | ||||||||||
| 1 | Aston Villa | 6 | 6 | 0 | 0 | 12 | 1 | +11 | 18 | Direct |
| 2 | West Ham | 6 | 5 | 1 | 0 | 20 | 4 | +16 | 16 | Direct |
| 3 | Jagiellonia Bialystok | 6 | 5 | 0 | 1 | 18 | 6 | +12 | 15 | Direct |
| 4 | Drogheda | 6 | 5 | 0 | 1 | 19 | 9 | +10 | 15 | Direct |
| 5 | Banik Ostrava | 6 | 5 | 0 | 1 | 17 | 7 | +10 | 15 | Direct |
| 6 | FC Runavik | 6 | 4 | 2 | 0 | 16 | 10 | +6 | 14 | Direct |
| 7 | Flora Tallinn | 6 | 4 | 1 | 1 | 10 | 5 | +5 | 13 | Direct |
| 8 | Differdange | 6 | 4 | 0 | 2 | 13 | 10 | +3 | 12 | Direct |
| Knockout Playoff Round | ||||||||||
| 9 | Lazio 2 | 6 | 4 | 0 | 2 | 13 | 12 | +1 | 12 | Playoff |
| 10 | Aberdeen | 6 | 3 | 2 | 1 | 13 | 9 | +4 | 11 | Playoff |
| 11 | Europa FC | 6 | 3 | 2 | 1 | 12 | 10 | +2 | 11 | Playoff |
| 12 | Fiorentina 2 | 6 | 3 | 2 | 1 | 10 | 8 | +2 | 11 | Playoff |
| 13 | Panathinaikos 2 | 6 | 3 | 1 | 2 | 17 | 12 | +5 | 10 | Playoff |
| 14 | PAOK 2 | 6 | 3 | 1 | 2 | 16 | 11 | +5 | 10 | Playoff |
| 15 | Rapid Wien | 6 | 3 | 1 | 2 | 16 | 12 | +4 | 10 | Playoff |
| 16 | Trabzonspor | 6 | 3 | 1 | 2 | 14 | 12 | +2 | 10 | Playoff |
| 17 | Real Betis 2 | 6 | 2 | 3 | 1 | 10 | 9 | +1 | 9 | Playoff |
| 18 | Lyon 2 | 6 | 2 | 2 | 2 | 12 | 11 | +1 | 8 | Playoff |
| 19 | FC Santa Coloma | 6 | 2 | 1 | 3 | 10 | 7 | +3 | 7 | Playoff |
| 20 | Lincoln Red Imps | 6 | 2 | 1 | 3 | 12 | 12 | 0 | 7 | Playoff |
| 21 | FCSB | 6 | 2 | 1 | 3 | 10 | 14 | -4 | 7 | Playoff |
| 22 | Cercle Brugge | 6 | 2 | 1 | 3 | 5 | 15 | -10 | 7 | Playoff |
| 23 | Mosta FC | 6 | 2 | 0 | 4 | 9 | 12 | -3 | 6 | Playoff |
| 24 | HB Torshavn | 6 | 2 | 0 | 4 | 13 | 17 | -4 | 6 | Playoff |
| Eliminated | ||||||||||
| 25 | Birkirkara 2 | 6 | 2 | 0 | 4 | 6 | 10 | -4 | 6 | Out |
| 26 | Riga FC | 6 | 2 | 0 | 4 | 9 | 17 | -8 | 6 | Out |
| 27 | Rennes 2 | 6 | 1 | 2 | 3 | 6 | 10 | -4 | 5 | Out |
| 28 | Kayserispor | 6 | 1 | 2 | 3 | 7 | 13 | -6 | 5 | Out |
| 29 | Metta LU | 6 | 1 | 1 | 4 | 8 | 11 | -3 | 4 | Out |
| 30 | Red Star | 6 | 0 | 4 | 2 | 7 | 11 | -4 | 4 | Out |
| 31 | Sivasspor | 6 | 1 | 1 | 4 | 6 | 14 | -8 | 4 | Out |
| 32 | Anderlecht 2 | 6 | 1 | 0 | 5 | 7 | 16 | -9 | 3 | Out |
| 33 | Real Sociedad 2 | 6 | 1 | 0 | 5 | 7 | 19 | -12 | 3 | Out |
| 34 | Gent 2 | 6 | 0 | 2 | 4 | 7 | 15 | -8 | 2 | Out |
| 35 | Lech Poznan | 6 | 0 | 2 | 4 | 7 | 15 | -8 | 2 | Out |
| 36 | Brondby | 6 | 0 | 1 | 5 | 5 | 13 | -8 | 1 | Out |