| Round of 16 — Direct Qualification | ||||||||||
| 1 | Villarreal | 8 | 7 | 1 | 0 | 27 | 5 | +22 | 22 | Direct |
| 2 | Monaco | 8 | 7 | 1 | 0 | 21 | 5 | +16 | 22 | Direct |
| 3 | Lyon | 8 | 6 | 2 | 0 | 17 | 5 | +12 | 20 | Direct |
| 4 | Tottenham | 8 | 6 | 1 | 1 | 22 | 5 | +17 | 19 | Direct |
| 5 | Valencia | 8 | 6 | 1 | 1 | 21 | 6 | +15 | 19 | Direct |
| 6 | Rennes | 8 | 6 | 1 | 1 | 21 | 10 | +11 | 19 | Direct |
| 7 | Vitoria SC | 8 | 6 | 0 | 2 | 20 | 10 | +10 | 18 | Direct |
| 8 | Linfield | 8 | 5 | 3 | 0 | 22 | 13 | +9 | 18 | Direct |
| Knockout Playoff Round | ||||||||||
| 9 | Braga | 8 | 5 | 2 | 1 | 22 | 10 | +12 | 17 | Playoff |
| 10 | Shamrock Rovers | 8 | 5 | 2 | 1 | 25 | 18 | +7 | 17 | Playoff |
| 11 | Teuta | 8 | 5 | 0 | 3 | 15 | 16 | -1 | 15 | Playoff |
| 12 | Vitesse | 8 | 4 | 2 | 2 | 23 | 16 | +7 | 14 | Playoff |
| 13 | Hajduk Split | 8 | 4 | 2 | 2 | 17 | 12 | +5 | 14 | Playoff |
| 14 | FK Suduva | 8 | 4 | 1 | 3 | 11 | 6 | +5 | 13 | Playoff |
| 15 | Augsburg | 8 | 4 | 1 | 3 | 19 | 15 | +4 | 13 | Playoff |
| 16 | Copenhagen | 8 | 3 | 2 | 3 | 16 | 18 | -2 | 11 | Playoff |
| 17 | Besiktas | 8 | 2 | 4 | 2 | 13 | 13 | 0 | 10 | Playoff |
| 18 | Slovan Bratislava | 8 | 3 | 1 | 4 | 17 | 20 | -3 | 10 | Playoff |
| 19 | Glenavon | 8 | 3 | 1 | 4 | 16 | 19 | -3 | 10 | Playoff |
| 20 | Rapid Wien 2 | 8 | 3 | 1 | 4 | 11 | 15 | -4 | 10 | Playoff |
| 21 | Eintracht Frankfurt | 8 | 3 | 1 | 4 | 13 | 20 | -7 | 10 | Playoff |
| 22 | Flora Tallinn | 8 | 2 | 3 | 3 | 13 | 16 | -3 | 9 | Playoff |
| 23 | Young Boys | 8 | 3 | 0 | 5 | 11 | 17 | -6 | 9 | Playoff |
| 24 | Slavia Prague 2 | 8 | 3 | 0 | 5 | 13 | 23 | -10 | 9 | Playoff |
| Eliminated | ||||||||||
| 25 | Sfintul Gheorghe | 8 | 2 | 2 | 4 | 15 | 17 | -2 | 8 | Out |
| 26 | Slavia Prague | 8 | 2 | 2 | 4 | 9 | 14 | -5 | 8 | Out |
| 27 | Manchester United | 8 | 1 | 3 | 4 | 13 | 16 | -3 | 6 | Out |
| 28 | Ajax 2 | 8 | 1 | 3 | 4 | 8 | 16 | -8 | 6 | Out |
| 29 | F91 Dudelange | 8 | 1 | 2 | 5 | 17 | 21 | -4 | 5 | Out |
| 30 | Club Brugge 2 | 8 | 1 | 2 | 5 | 10 | 18 | -8 | 5 | Out |
| 31 | Real Betis | 8 | 1 | 2 | 5 | 16 | 25 | -9 | 5 | Out |
| 32 | Sparta Prague 2 | 8 | 1 | 1 | 6 | 3 | 15 | -12 | 4 | Out |
| 33 | Lincoln Red Imps | 8 | 1 | 1 | 6 | 8 | 21 | -13 | 4 | Out |
| 34 | FCSB | 8 | 1 | 0 | 7 | 6 | 18 | -12 | 3 | Out |
| 35 | AS Roma | 8 | 0 | 2 | 6 | 6 | 27 | -21 | 2 | Out |
| 36 | CFR Cluj | 8 | 0 | 1 | 7 | 13 | 29 | -16 | 1 | Out |