| Round of 16 — Direct Qualification | ||||||||||
| 1 | Tottenham | 8 | 8 | 0 | 0 | 25 | 10 | +15 | 24 | Direct |
| 2 | Monaco | 8 | 7 | 1 | 0 | 32 | 4 | +28 | 22 | Direct |
| 3 | Lyon | 8 | 6 | 1 | 1 | 27 | 11 | +16 | 19 | Direct |
| 4 | Villarreal | 8 | 6 | 1 | 1 | 20 | 11 | +9 | 19 | Direct |
| 5 | Braga | 8 | 5 | 3 | 0 | 19 | 4 | +15 | 18 | Direct |
| 6 | Valencia | 8 | 5 | 2 | 1 | 17 | 8 | +9 | 17 | Direct |
| 7 | CFR Cluj | 8 | 5 | 2 | 1 | 26 | 18 | +8 | 17 | Direct |
| 8 | Augsburg | 8 | 5 | 1 | 2 | 19 | 10 | +9 | 16 | Direct |
| Knockout Playoff Round | ||||||||||
| 9 | Olympiacos | 8 | 4 | 3 | 1 | 18 | 9 | +9 | 15 | Playoff |
| 10 | Sheriff | 8 | 4 | 2 | 2 | 16 | 15 | +1 | 14 | Playoff |
| 11 | Slavia Prague 2 | 8 | 4 | 1 | 3 | 16 | 11 | +5 | 13 | Playoff |
| 12 | Valletta | 8 | 4 | 1 | 3 | 21 | 19 | +2 | 13 | Playoff |
| 13 | Rennes | 8 | 4 | 1 | 3 | 15 | 14 | +1 | 13 | Playoff |
| 14 | Motherwell | 8 | 4 | 0 | 4 | 19 | 21 | -2 | 12 | Playoff |
| 15 | Manchester United | 8 | 4 | 0 | 4 | 14 | 20 | -6 | 12 | Playoff |
| 16 | Standard Liege | 8 | 3 | 2 | 3 | 16 | 16 | 0 | 11 | Playoff |
| 17 | Hajduk Split | 8 | 3 | 2 | 3 | 17 | 19 | -2 | 11 | Playoff |
| 18 | Sutjeska | 8 | 3 | 2 | 3 | 16 | 19 | -3 | 11 | Playoff |
| 19 | Club Brugge 2 | 8 | 3 | 1 | 4 | 14 | 14 | 0 | 10 | Playoff |
| 20 | Sliema Wanderers | 8 | 3 | 1 | 4 | 16 | 17 | -1 | 10 | Playoff |
| 21 | Vitesse | 8 | 3 | 1 | 4 | 16 | 18 | -2 | 10 | Playoff |
| 22 | Real Betis | 8 | 3 | 1 | 4 | 11 | 14 | -3 | 10 | Playoff |
| 23 | Rapid Wien 2 | 8 | 3 | 1 | 4 | 10 | 19 | -9 | 10 | Playoff |
| 24 | Glenavon | 8 | 2 | 2 | 4 | 14 | 19 | -5 | 8 | Playoff |
| Eliminated | ||||||||||
| 25 | Hearts | 8 | 2 | 2 | 4 | 11 | 17 | -6 | 8 | Out |
| 26 | Eintracht Frankfurt | 8 | 2 | 2 | 4 | 9 | 17 | -8 | 8 | Out |
| 27 | Sparta Prague 2 | 8 | 1 | 4 | 3 | 19 | 21 | -2 | 7 | Out |
| 28 | Lincoln Red Imps | 8 | 2 | 1 | 5 | 15 | 20 | -5 | 7 | Out |
| 29 | Besiktas | 8 | 2 | 1 | 5 | 4 | 19 | -15 | 7 | Out |
| 30 | Panevezys | 8 | 2 | 0 | 6 | 18 | 22 | -4 | 6 | Out |
| 31 | AS Roma | 8 | 2 | 0 | 6 | 12 | 17 | -5 | 6 | Out |
| 32 | FC Santa Coloma | 8 | 1 | 3 | 4 | 12 | 19 | -7 | 6 | Out |
| 33 | Ajax 2 | 8 | 1 | 2 | 5 | 10 | 21 | -11 | 5 | Out |
| 34 | Shamrock Rovers | 8 | 1 | 1 | 6 | 14 | 23 | -9 | 4 | Out |
| 35 | Paide | 8 | 1 | 1 | 6 | 16 | 27 | -11 | 4 | Out |
| 36 | Panathinaikos | 8 | 0 | 3 | 5 | 9 | 20 | -11 | 3 | Out |