| Round of 16 — Direct Qualification | ||||||||||
| 1 | Monaco | 8 | 8 | 0 | 0 | 25 | 3 | +22 | 24 | Direct |
| 2 | Rennes | 8 | 7 | 0 | 1 | 23 | 6 | +17 | 21 | Direct |
| 3 | Braga | 8 | 6 | 2 | 0 | 22 | 9 | +13 | 20 | Direct |
| 4 | Lyon | 8 | 6 | 1 | 1 | 29 | 7 | +22 | 19 | Direct |
| 5 | Augsburg | 8 | 6 | 1 | 1 | 25 | 8 | +17 | 19 | Direct |
| 6 | Tottenham | 8 | 6 | 1 | 1 | 17 | 6 | +11 | 19 | Direct |
| 7 | Ludogorets | 8 | 5 | 1 | 2 | 18 | 15 | +3 | 16 | Direct |
| 8 | Waterford | 8 | 5 | 1 | 2 | 21 | 19 | +2 | 16 | Direct |
| Knockout Playoff Round | ||||||||||
| 9 | Villarreal | 8 | 4 | 2 | 2 | 18 | 9 | +9 | 14 | Playoff |
| 10 | Skenderbeu | 8 | 4 | 1 | 3 | 14 | 12 | +2 | 13 | Playoff |
| 11 | Copenhagen | 8 | 4 | 1 | 3 | 13 | 16 | -3 | 13 | Playoff |
| 12 | Eintracht Frankfurt | 8 | 3 | 3 | 2 | 18 | 9 | +9 | 12 | Playoff |
| 13 | RFS | 8 | 4 | 0 | 4 | 14 | 17 | -3 | 12 | Playoff |
| 14 | Slovan Bratislava | 8 | 3 | 2 | 3 | 20 | 12 | +8 | 11 | Playoff |
| 15 | Valencia | 8 | 2 | 5 | 1 | 15 | 13 | +2 | 11 | Playoff |
| 16 | Sligo Rovers | 8 | 3 | 2 | 3 | 16 | 15 | +1 | 11 | Playoff |
| 17 | Standard Liege | 8 | 3 | 2 | 3 | 16 | 17 | -1 | 11 | Playoff |
| 18 | Sparta Prague 2 | 8 | 3 | 2 | 3 | 11 | 12 | -1 | 11 | Playoff |
| 19 | FK Suduva | 8 | 3 | 1 | 4 | 13 | 13 | 0 | 10 | Playoff |
| 20 | CSKA Sofia | 8 | 3 | 1 | 4 | 11 | 17 | -6 | 10 | Playoff |
| 21 | AZ Alkmaar | 8 | 3 | 1 | 4 | 7 | 15 | -8 | 10 | Playoff |
| 22 | Panevezys | 8 | 3 | 0 | 5 | 13 | 14 | -1 | 9 | Playoff |
| 23 | Ajax 2 | 8 | 2 | 2 | 4 | 18 | 18 | 0 | 8 | Playoff |
| 24 | Dundalk | 8 | 2 | 2 | 4 | 6 | 11 | -5 | 8 | Playoff |
| Eliminated | ||||||||||
| 25 | Sliema Wanderers | 8 | 2 | 2 | 4 | 15 | 21 | -6 | 8 | Out |
| 26 | Real Betis | 8 | 1 | 4 | 3 | 8 | 15 | -7 | 7 | Out |
| 27 | Manchester United | 8 | 2 | 1 | 5 | 12 | 21 | -9 | 7 | Out |
| 28 | Slavia Prague 2 | 8 | 2 | 1 | 5 | 12 | 23 | -11 | 7 | Out |
| 29 | Rapid Wien 2 | 8 | 2 | 1 | 5 | 15 | 27 | -12 | 7 | Out |
| 30 | Club Brugge 2 | 8 | 2 | 1 | 5 | 10 | 24 | -14 | 7 | Out |
| 31 | Hibernians | 8 | 1 | 3 | 4 | 14 | 17 | -3 | 6 | Out |
| 32 | Maccabi Tel Aviv | 8 | 2 | 0 | 6 | 10 | 17 | -7 | 6 | Out |
| 33 | Glenavon | 8 | 1 | 3 | 4 | 11 | 19 | -8 | 6 | Out |
| 34 | AS Roma | 8 | 1 | 3 | 4 | 8 | 20 | -12 | 6 | Out |
| 35 | Besiktas | 8 | 1 | 2 | 5 | 14 | 22 | -8 | 5 | Out |
| 36 | Vitesse | 8 | 1 | 1 | 6 | 7 | 20 | -13 | 4 | Out |