| Round of 16 — Direct Qualification | ||||||||||
| 1 | West Ham | 6 | 4 | 2 | 0 | 18 | 5 | +13 | 14 | Direct |
| 2 | Petrocub | 6 | 4 | 2 | 0 | 16 | 9 | +7 | 14 | Direct |
| 3 | Brondby | 6 | 4 | 1 | 1 | 16 | 7 | +9 | 13 | Direct |
| 4 | FK Liepaja | 6 | 4 | 1 | 1 | 12 | 8 | +4 | 13 | Direct |
| 5 | Real Sociedad 2 | 6 | 4 | 0 | 2 | 18 | 11 | +7 | 12 | Direct |
| 6 | Sivasspor | 6 | 4 | 0 | 2 | 13 | 6 | +7 | 12 | Direct |
| 7 | Differdange | 6 | 4 | 0 | 2 | 14 | 8 | +6 | 12 | Direct |
| 8 | Kayserispor | 6 | 4 | 0 | 2 | 10 | 7 | +3 | 12 | Direct |
| Knockout Playoff Round | ||||||||||
| 9 | Buducnost | 6 | 3 | 2 | 1 | 12 | 9 | +3 | 11 | Playoff |
| 10 | Lyon 2 | 6 | 3 | 2 | 1 | 11 | 8 | +3 | 11 | Playoff |
| 11 | Aston Villa | 6 | 3 | 1 | 2 | 13 | 8 | +5 | 10 | Playoff |
| 12 | Tirana | 6 | 3 | 1 | 2 | 11 | 7 | +4 | 10 | Playoff |
| 13 | Midtjylland | 6 | 3 | 1 | 2 | 14 | 12 | +2 | 10 | Playoff |
| 14 | Ballymena United | 6 | 3 | 1 | 2 | 10 | 8 | +2 | 10 | Playoff |
| 15 | Sturm Graz | 6 | 3 | 1 | 2 | 14 | 15 | -1 | 10 | Playoff |
| 16 | Real Betis 2 | 6 | 3 | 1 | 2 | 9 | 10 | -1 | 10 | Playoff |
| 17 | Fiorentina 2 | 6 | 3 | 0 | 3 | 16 | 14 | +2 | 9 | Playoff |
| 18 | Valur Reykjavik | 6 | 3 | 0 | 3 | 15 | 14 | +1 | 9 | Playoff |
| 19 | FC Santa Coloma | 6 | 3 | 0 | 3 | 15 | 19 | -4 | 9 | Playoff |
| 20 | Waterford | 6 | 2 | 2 | 2 | 13 | 8 | +5 | 8 | Playoff |
| 21 | Jagiellonia Bialystok | 6 | 2 | 2 | 2 | 13 | 12 | +1 | 8 | Playoff |
| 22 | Lazio 2 | 6 | 2 | 2 | 2 | 13 | 14 | -1 | 8 | Playoff |
| 23 | PAOK 2 | 6 | 2 | 2 | 2 | 8 | 11 | -3 | 8 | Playoff |
| 24 | Vllaznia | 6 | 2 | 1 | 3 | 13 | 15 | -2 | 7 | Playoff |
| Eliminated | ||||||||||
| 25 | Panathinaikos 2 | 6 | 2 | 1 | 3 | 10 | 12 | -2 | 7 | Out |
| 26 | Tre Fiori | 6 | 2 | 1 | 3 | 10 | 17 | -7 | 7 | Out |
| 27 | Anderlecht 2 | 6 | 2 | 0 | 4 | 13 | 10 | +3 | 6 | Out |
| 28 | Europa FC | 6 | 1 | 3 | 2 | 10 | 13 | -3 | 6 | Out |
| 29 | Valletta | 6 | 1 | 2 | 3 | 10 | 12 | -2 | 5 | Out |
| 30 | Gent 2 | 6 | 1 | 2 | 3 | 10 | 13 | -3 | 5 | Out |
| 31 | Red Star | 6 | 1 | 1 | 4 | 10 | 17 | -7 | 4 | Out |
| 32 | RFS | 6 | 1 | 1 | 4 | 4 | 19 | -15 | 4 | Out |
| 33 | Lech Poznan | 6 | 0 | 3 | 3 | 8 | 15 | -7 | 3 | Out |
| 34 | Bohemian | 6 | 1 | 0 | 5 | 8 | 17 | -9 | 3 | Out |
| 35 | Zalgiris Vilnius | 6 | 1 | 0 | 5 | 6 | 16 | -10 | 3 | Out |
| 36 | Rennes 2 | 6 | 0 | 1 | 5 | 5 | 15 | -10 | 1 | Out |