| Round of 16 — Direct Qualification | ||||||||||
| 1 | Villarreal | 8 | 7 | 1 | 0 | 28 | 5 | +23 | 22 | Direct |
| 2 | Lyon | 8 | 7 | 1 | 0 | 27 | 7 | +20 | 22 | Direct |
| 3 | Braga | 8 | 6 | 1 | 1 | 22 | 6 | +16 | 19 | Direct |
| 4 | Rennes | 8 | 6 | 1 | 1 | 20 | 9 | +11 | 19 | Direct |
| 5 | Copenhagen | 8 | 6 | 1 | 1 | 19 | 10 | +9 | 19 | Direct |
| 6 | Valencia | 8 | 6 | 0 | 2 | 19 | 12 | +7 | 18 | Direct |
| 7 | Tottenham | 8 | 5 | 2 | 1 | 17 | 7 | +10 | 17 | Direct |
| 8 | Vitesse | 8 | 5 | 2 | 1 | 17 | 8 | +9 | 17 | Direct |
| Knockout Playoff Round | ||||||||||
| 9 | Augsburg | 8 | 5 | 2 | 1 | 12 | 7 | +5 | 17 | Playoff |
| 10 | Monaco | 8 | 5 | 1 | 2 | 15 | 7 | +8 | 16 | Playoff |
| 11 | Dundalk | 8 | 4 | 3 | 1 | 17 | 8 | +9 | 15 | Playoff |
| 12 | Club Brugge 2 | 8 | 4 | 2 | 2 | 10 | 12 | -2 | 14 | Playoff |
| 13 | Ordabasy | 8 | 3 | 4 | 1 | 16 | 11 | +5 | 13 | Playoff |
| 14 | Riga FC | 8 | 4 | 1 | 3 | 20 | 18 | +2 | 13 | Playoff |
| 15 | Real Betis | 8 | 4 | 1 | 3 | 15 | 16 | -1 | 13 | Playoff |
| 16 | Sparta Prague 2 | 8 | 3 | 3 | 2 | 18 | 12 | +6 | 12 | Playoff |
| 17 | Paide | 8 | 4 | 0 | 4 | 20 | 23 | -3 | 12 | Playoff |
| 18 | FC Andorra | 8 | 3 | 2 | 3 | 10 | 10 | 0 | 11 | Playoff |
| 19 | AS Roma | 8 | 3 | 2 | 3 | 15 | 17 | -2 | 11 | Playoff |
| 20 | Rapid Wien | 8 | 2 | 4 | 2 | 15 | 13 | +2 | 10 | Playoff |
| 21 | Nomme Kalju | 8 | 3 | 1 | 4 | 12 | 15 | -3 | 10 | Playoff |
| 22 | Rapid Wien 2 | 8 | 3 | 0 | 5 | 19 | 19 | 0 | 9 | Playoff |
| 23 | Waterford | 8 | 2 | 3 | 3 | 17 | 17 | 0 | 9 | Playoff |
| 24 | Basel | 8 | 2 | 3 | 3 | 13 | 16 | -3 | 9 | Playoff |
| Eliminated | ||||||||||
| 25 | La Fiorita | 8 | 3 | 0 | 5 | 16 | 23 | -7 | 9 | Out |
| 26 | Eintracht Frankfurt | 8 | 2 | 2 | 4 | 12 | 20 | -8 | 8 | Out |
| 27 | Rosenborg | 8 | 2 | 1 | 5 | 11 | 18 | -7 | 7 | Out |
| 28 | Besiktas | 8 | 1 | 3 | 4 | 11 | 16 | -5 | 6 | Out |
| 29 | Ajax 2 | 8 | 2 | 0 | 6 | 13 | 19 | -6 | 6 | Out |
| 30 | RFS | 8 | 2 | 0 | 6 | 8 | 20 | -12 | 6 | Out |
| 31 | Gent | 8 | 1 | 2 | 5 | 12 | 19 | -7 | 5 | Out |
| 32 | Manchester United | 8 | 1 | 1 | 6 | 8 | 21 | -13 | 4 | Out |
| 33 | Sliema Wanderers | 8 | 1 | 1 | 6 | 10 | 26 | -16 | 4 | Out |
| 34 | Slavia Prague 2 | 8 | 1 | 0 | 7 | 13 | 21 | -8 | 3 | Out |
| 35 | Vikingur Reykjavik | 8 | 0 | 1 | 7 | 8 | 24 | -16 | 1 | Out |
| 36 | Midtjylland | 8 | 0 | 0 | 8 | 3 | 26 | -23 | 0 | Out |