| Round of 16 — Direct Qualification | ||||||||||
| 1 | Lyon | 8 | 8 | 0 | 0 | 29 | 9 | +20 | 24 | Direct |
| 2 | Braga | 8 | 7 | 1 | 0 | 28 | 6 | +22 | 22 | Direct |
| 3 | Rennes | 8 | 7 | 0 | 1 | 27 | 7 | +20 | 21 | Direct |
| 4 | Monaco | 8 | 6 | 1 | 1 | 19 | 10 | +9 | 19 | Direct |
| 5 | Vitesse | 8 | 6 | 1 | 1 | 19 | 10 | +9 | 19 | Direct |
| 6 | Tottenham | 8 | 5 | 2 | 1 | 16 | 7 | +9 | 17 | Direct |
| 7 | Villarreal | 8 | 5 | 1 | 2 | 18 | 7 | +11 | 16 | Direct |
| 8 | CSKA Sofia | 8 | 5 | 1 | 2 | 16 | 13 | +3 | 16 | Direct |
| Knockout Playoff Round | ||||||||||
| 9 | Vojvodina | 8 | 4 | 2 | 2 | 18 | 12 | +6 | 14 | Playoff |
| 10 | Brondby | 8 | 4 | 1 | 3 | 22 | 15 | +7 | 13 | Playoff |
| 11 | Augsburg | 8 | 3 | 4 | 1 | 17 | 12 | +5 | 13 | Playoff |
| 12 | Valencia | 8 | 3 | 4 | 1 | 13 | 12 | +1 | 13 | Playoff |
| 13 | Slavia Prague 2 | 8 | 2 | 5 | 1 | 22 | 18 | +4 | 11 | Playoff |
| 14 | Paide | 8 | 3 | 2 | 3 | 13 | 13 | 0 | 11 | Playoff |
| 15 | Club Brugge 2 | 8 | 3 | 1 | 4 | 19 | 17 | +2 | 10 | Playoff |
| 16 | Ajax 2 | 8 | 3 | 1 | 4 | 17 | 21 | -4 | 10 | Playoff |
| 17 | Utrecht | 8 | 3 | 1 | 4 | 17 | 24 | -7 | 10 | Playoff |
| 18 | Levadia Tallinn | 8 | 2 | 3 | 3 | 19 | 18 | +1 | 9 | Playoff |
| 19 | Cercle Brugge | 8 | 2 | 3 | 3 | 11 | 13 | -2 | 9 | Playoff |
| 20 | FK Liepaja | 8 | 3 | 0 | 5 | 15 | 19 | -4 | 9 | Playoff |
| 21 | Rapid Wien 2 | 8 | 3 | 0 | 5 | 19 | 27 | -8 | 9 | Playoff |
| 22 | Europa FC | 8 | 3 | 0 | 5 | 13 | 25 | -12 | 9 | Playoff |
| 23 | Manchester United | 8 | 2 | 2 | 4 | 13 | 15 | -2 | 8 | Playoff |
| 24 | Tre Fiori | 8 | 1 | 5 | 2 | 10 | 13 | -3 | 8 | Playoff |
| Eliminated | ||||||||||
| 25 | Besiktas | 8 | 2 | 2 | 4 | 13 | 18 | -5 | 8 | Out |
| 26 | Molde | 8 | 2 | 2 | 4 | 11 | 17 | -6 | 8 | Out |
| 27 | Eintracht Frankfurt | 8 | 2 | 2 | 4 | 9 | 16 | -7 | 8 | Out |
| 28 | Sparta Prague 2 | 8 | 2 | 2 | 4 | 12 | 20 | -8 | 8 | Out |
| 29 | Rosenborg | 8 | 2 | 2 | 4 | 9 | 17 | -8 | 8 | Out |
| 30 | AS Roma | 8 | 2 | 2 | 4 | 13 | 24 | -11 | 8 | Out |
| 31 | Ordabasy | 8 | 2 | 1 | 5 | 14 | 21 | -7 | 7 | Out |
| 32 | Petrocub | 8 | 2 | 1 | 5 | 12 | 20 | -8 | 7 | Out |
| 33 | Flora Tallinn | 8 | 1 | 3 | 4 | 10 | 14 | -4 | 6 | Out |
| 34 | Real Betis | 8 | 2 | 0 | 6 | 12 | 20 | -8 | 6 | Out |
| 35 | Motherwell | 8 | 1 | 2 | 5 | 15 | 20 | -5 | 5 | Out |
| 36 | Hibernians | 8 | 1 | 0 | 7 | 11 | 21 | -10 | 3 | Out |