| Round of 16 — Direct Qualification | ||||||||||
| 1 | Monaco | 8 | 8 | 0 | 0 | 22 | 2 | +20 | 24 | Direct |
| 2 | Rennes | 8 | 7 | 1 | 0 | 22 | 5 | +17 | 22 | Direct |
| 3 | Lyon | 8 | 6 | 2 | 0 | 28 | 3 | +25 | 20 | Direct |
| 4 | Tottenham | 8 | 6 | 2 | 0 | 21 | 10 | +11 | 20 | Direct |
| 5 | Braga | 8 | 6 | 1 | 1 | 17 | 7 | +10 | 19 | Direct |
| 6 | Villarreal | 8 | 5 | 2 | 1 | 22 | 7 | +15 | 17 | Direct |
| 7 | RFS | 8 | 5 | 2 | 1 | 25 | 15 | +10 | 17 | Direct |
| 8 | Augsburg | 8 | 5 | 2 | 1 | 16 | 6 | +10 | 17 | Direct |
| Knockout Playoff Round | ||||||||||
| 9 | Valencia | 8 | 5 | 1 | 2 | 20 | 11 | +9 | 16 | Playoff |
| 10 | Sheriff | 8 | 5 | 1 | 2 | 18 | 13 | +5 | 16 | Playoff |
| 11 | Riga FC | 8 | 4 | 2 | 2 | 26 | 18 | +8 | 14 | Playoff |
| 12 | AS Roma | 8 | 4 | 1 | 3 | 17 | 15 | +2 | 13 | Playoff |
| 13 | Real Betis | 8 | 3 | 3 | 2 | 15 | 15 | 0 | 12 | Playoff |
| 14 | Panathinaikos | 8 | 4 | 0 | 4 | 14 | 20 | -6 | 12 | Playoff |
| 15 | FC Santa Coloma | 8 | 3 | 2 | 3 | 17 | 18 | -1 | 11 | Playoff |
| 16 | Hibernians | 8 | 3 | 2 | 3 | 13 | 17 | -4 | 11 | Playoff |
| 17 | Europa FC | 8 | 3 | 1 | 4 | 16 | 14 | +2 | 10 | Playoff |
| 18 | LASK | 8 | 3 | 1 | 4 | 16 | 16 | 0 | 10 | Playoff |
| 19 | Sparta Prague 2 | 8 | 3 | 1 | 4 | 15 | 15 | 0 | 10 | Playoff |
| 20 | Levadia Tallinn | 8 | 3 | 1 | 4 | 16 | 20 | -4 | 10 | Playoff |
| 21 | Club Brugge 2 | 8 | 3 | 1 | 4 | 14 | 18 | -4 | 10 | Playoff |
| 22 | FK Suduva | 8 | 3 | 1 | 4 | 15 | 20 | -5 | 10 | Playoff |
| 23 | Valletta | 8 | 2 | 3 | 3 | 11 | 18 | -7 | 9 | Playoff |
| 24 | Glenavon | 8 | 2 | 2 | 4 | 17 | 18 | -1 | 8 | Playoff |
| Eliminated | ||||||||||
| 25 | PAOK | 8 | 2 | 2 | 4 | 10 | 14 | -4 | 8 | Out |
| 26 | Molde | 8 | 2 | 2 | 4 | 9 | 17 | -8 | 8 | Out |
| 27 | Ajax 2 | 8 | 2 | 1 | 5 | 13 | 17 | -4 | 7 | Out |
| 28 | Rapid Wien 2 | 8 | 2 | 1 | 5 | 11 | 16 | -5 | 7 | Out |
| 29 | Vitesse | 8 | 2 | 1 | 5 | 8 | 19 | -11 | 7 | Out |
| 30 | Drogheda | 8 | 2 | 0 | 6 | 11 | 21 | -10 | 6 | Out |
| 31 | Gent | 8 | 2 | 0 | 6 | 11 | 22 | -11 | 6 | Out |
| 32 | Slavia Prague 2 | 8 | 1 | 2 | 5 | 11 | 20 | -9 | 5 | Out |
| 33 | Manchester United | 8 | 1 | 2 | 5 | 14 | 25 | -11 | 5 | Out |
| 34 | Midtjylland | 8 | 1 | 1 | 6 | 10 | 18 | -8 | 4 | Out |
| 35 | Eintracht Frankfurt | 8 | 1 | 1 | 6 | 9 | 24 | -15 | 4 | Out |
| 36 | Hamrun Spartans | 8 | 1 | 0 | 7 | 5 | 21 | -16 | 3 | Out |