| Position | Club | P | W | D | L | GF | GA | GD | Pts | Status |
|---|---|---|---|---|---|---|---|---|---|---|
| Round of 16 — Direct Qualification | ||||||||||
| 1 | Lyon | 8 | 7 | 1 | 0 | 21 | 7 | +14 | 22 | Direct |
| 2 | Monaco | 8 | 7 | 1 | 0 | 19 | 5 | +14 | 22 | Direct |
| 3 | Rennes | 8 | 6 | 2 | 0 | 24 | 5 | +19 | 20 | Direct |
| 4 | Tottenham | 8 | 6 | 2 | 0 | 24 | 5 | +19 | 20 | Direct |
| 5 | Braga | 8 | 6 | 2 | 0 | 17 | 6 | +11 | 20 | Direct |
| 6 | Villarreal | 8 | 6 | 1 | 1 | 13 | 7 | +6 | 19 | Direct |
| 7 | Valencia | 8 | 6 | 0 | 2 | 22 | 7 | +15 | 18 | Direct |
| 8 | Augsburg | 8 | 4 | 4 | 0 | 17 | 8 | +9 | 16 | Direct |
| Knockout Playoff Round | ||||||||||
| 9 | Utrecht | 8 | 5 | 1 | 2 | 21 | 13 | +8 | 16 | Playoff |
| 10 | Levadia Tallinn | 8 | 5 | 1 | 2 | 19 | 14 | +5 | 16 | Playoff |
| 11 | Genk | 8 | 4 | 2 | 2 | 14 | 9 | +5 | 14 | Playoff |
| 12 | Slavia Prague | 8 | 4 | 1 | 3 | 19 | 15 | +4 | 13 | Playoff |
| 13 | RFS | 8 | 4 | 1 | 3 | 19 | 23 | -4 | 13 | Playoff |
| 14 | FC Andorra | 8 | 3 | 3 | 2 | 12 | 11 | +1 | 12 | Playoff |
| 15 | Flora Tallinn | 8 | 4 | 0 | 4 | 17 | 17 | 0 | 12 | Playoff |
| 16 | Basel | 8 | 4 | 0 | 4 | 13 | 13 | 0 | 12 | Playoff |
| 17 | Elbasani | 8 | 3 | 3 | 2 | 11 | 12 | -1 | 12 | Playoff |
| 18 | Paide | 8 | 3 | 2 | 3 | 15 | 15 | 0 | 11 | Playoff |
| 19 | Sparta Prague 2 | 8 | 3 | 2 | 3 | 14 | 15 | -1 | 11 | Playoff |
| 20 | Slavia Prague 2 | 8 | 2 | 4 | 2 | 12 | 14 | -2 | 10 | Playoff |
| 21 | Differdange | 8 | 3 | 1 | 4 | 13 | 17 | -4 | 10 | Playoff |
| 22 | Club Brugge 2 | 8 | 3 | 1 | 4 | 11 | 16 | -5 | 10 | Playoff |
| 23 | Ludogorets | 8 | 2 | 3 | 3 | 16 | 19 | -3 | 9 | Playoff |
| 24 | Rapid Wien 2 | 8 | 2 | 3 | 3 | 13 | 18 | -5 | 9 | Playoff |
| Eliminated | ||||||||||
| 25 | Standard Liege | 8 | 1 | 4 | 3 | 18 | 23 | -5 | 7 | Out |
| 26 | Ajax 2 | 8 | 2 | 1 | 5 | 14 | 21 | -7 | 7 | Out |
| 27 | Hajduk Split | 8 | 1 | 3 | 4 | 9 | 15 | -6 | 6 | Out |
| 28 | LASK | 8 | 1 | 3 | 4 | 21 | 28 | -7 | 6 | Out |
| 29 | Vitesse | 8 | 1 | 2 | 5 | 9 | 11 | -2 | 5 | Out |
| 30 | Eintracht Frankfurt | 8 | 1 | 2 | 5 | 15 | 22 | -7 | 5 | Out |
| 31 | Sfintul Gheorghe | 8 | 0 | 3 | 5 | 9 | 18 | -9 | 3 | Out |
| 32 | AS Roma | 8 | 0 | 3 | 5 | 7 | 16 | -9 | 3 | Out |
| 33 | CSKA Sofia | 8 | 1 | 0 | 7 | 9 | 24 | -15 | 3 | Out |
| 34 | Real Betis | 8 | 0 | 2 | 6 | 18 | 30 | -12 | 2 | Out |
| 35 | Panevezys | 8 | 0 | 2 | 6 | 5 | 17 | -12 | 2 | Out |
| 36 | Manchester United | 8 | 0 | 2 | 6 | 4 | 18 | -14 | 2 | Out |