| Round of 16 — Direct Qualification | ||||||||||
| 1 | Tottenham | 8 | 8 | 0 | 0 | 27 | 3 | +24 | 24 | Direct |
| 2 | Monaco | 8 | 8 | 0 | 0 | 20 | 2 | +18 | 24 | Direct |
| 3 | Villarreal | 8 | 8 | 0 | 0 | 21 | 5 | +16 | 24 | Direct |
| 4 | Rennes | 8 | 7 | 1 | 0 | 26 | 5 | +21 | 22 | Direct |
| 5 | Braga | 8 | 6 | 2 | 0 | 22 | 4 | +18 | 20 | Direct |
| 6 | Wisla Krakow | 8 | 5 | 1 | 2 | 21 | 10 | +11 | 16 | Direct |
| 7 | Sparta Prague 2 | 8 | 5 | 1 | 2 | 18 | 14 | +4 | 16 | Direct |
| 8 | Valencia | 8 | 5 | 0 | 3 | 21 | 9 | +12 | 15 | Direct |
| Knockout Playoff Round | ||||||||||
| 9 | Lyon | 8 | 4 | 3 | 1 | 19 | 12 | +7 | 15 | Playoff |
| 10 | Vitesse | 8 | 4 | 2 | 2 | 20 | 16 | +4 | 14 | Playoff |
| 11 | Ludogorets | 8 | 4 | 2 | 2 | 18 | 18 | 0 | 14 | Playoff |
| 12 | Sarajevo | 8 | 4 | 1 | 3 | 18 | 12 | +6 | 13 | Playoff |
| 13 | Riga FC | 8 | 4 | 1 | 3 | 12 | 8 | +4 | 13 | Playoff |
| 14 | Real Betis | 8 | 4 | 1 | 3 | 20 | 25 | -5 | 13 | Playoff |
| 15 | Augsburg | 8 | 4 | 0 | 4 | 6 | 10 | -4 | 12 | Playoff |
| 16 | Kairat | 8 | 4 | 0 | 4 | 11 | 18 | -7 | 12 | Playoff |
| 17 | Tre Fiori | 8 | 3 | 2 | 3 | 15 | 15 | 0 | 11 | Playoff |
| 18 | Rapid Wien | 8 | 3 | 2 | 3 | 9 | 16 | -7 | 11 | Playoff |
| 19 | Utrecht | 8 | 3 | 1 | 4 | 16 | 11 | +5 | 10 | Playoff |
| 20 | Vikingur Reykjavik | 8 | 3 | 1 | 4 | 22 | 19 | +3 | 10 | Playoff |
| 21 | Drogheda | 8 | 3 | 1 | 4 | 17 | 14 | +3 | 10 | Playoff |
| 22 | Ajax 2 | 8 | 3 | 1 | 4 | 16 | 21 | -5 | 10 | Playoff |
| 23 | AS Roma | 8 | 3 | 1 | 4 | 13 | 20 | -7 | 10 | Playoff |
| 24 | Glenavon | 8 | 3 | 0 | 5 | 13 | 15 | -2 | 9 | Playoff |
| Eliminated | ||||||||||
| 25 | Slavia Prague 2 | 8 | 2 | 2 | 4 | 13 | 19 | -6 | 8 | Out |
| 26 | Young Boys | 8 | 2 | 2 | 4 | 6 | 12 | -6 | 8 | Out |
| 27 | Club Brugge 2 | 8 | 2 | 2 | 4 | 10 | 17 | -7 | 8 | Out |
| 28 | Cercle Brugge | 8 | 2 | 0 | 6 | 12 | 16 | -4 | 6 | Out |
| 29 | Teuta | 8 | 2 | 0 | 6 | 15 | 20 | -5 | 6 | Out |
| 30 | Austria Wien | 8 | 2 | 0 | 6 | 11 | 18 | -7 | 6 | Out |
| 31 | Red Star | 8 | 1 | 2 | 5 | 8 | 19 | -11 | 5 | Out |
| 32 | Molde | 8 | 1 | 2 | 5 | 11 | 23 | -12 | 5 | Out |
| 33 | Eintracht Frankfurt | 8 | 1 | 2 | 5 | 6 | 23 | -17 | 5 | Out |
| 34 | Nomme Kalju | 8 | 1 | 1 | 6 | 11 | 21 | -10 | 4 | Out |
| 35 | Manchester United | 8 | 0 | 2 | 6 | 5 | 24 | -19 | 2 | Out |
| 36 | Rapid Wien 2 | 8 | 0 | 1 | 7 | 9 | 24 | -15 | 1 | Out |