| ROUND | C | Q1 | Q2 | Q3 | Q4 | R1 | R2 | QF | SF | F | ||||||||||||
| l1 | l2 | l1 | l2 | l1 | l2 | l1 | l2 | r1 | r2 | r3 | r4 | r5 | r6 | l1 | l2 | l1 | l2 | l1 | l2 | |||
| Season archive |
| Tuesday, 17 July 2012 | ||||||
| q2l1 |  HJK | 7-0 | KR | |||
| q2l1 |  Shamrock Rovers | 0-0 | Ekranas | |||
| q2l1 |  Slovan Liberec | 1-0 | Shakhter | |||
| q2l1 |  Flora | 0-2 | FC Basel | |||
| q2l1 |  Neftçi | 3-0 | Zestafoni | |||
| q2l1 |  Valletta | 1-4 | Partizan | |||
| q2l1 |  F91 Düdelingen | 1-0 | FC Salzburg | |||
| q2l1 |  MŠK Žilina | 1-0 | Hapoel Ironi Kiryat Shmona | |||
| q2l1 |  The New Saints | 0-0 | Helsingborg | |||
| q2l1 |  Skënderbeu | 1-0 | Debrecen | |||
| q2l1 |  Ulysses | 0-1 | Sheriff | |||
| Wednesday, 18 July 2012 | ||||||
| q2l1 |  Molde | 3-0 | JFK Ventspils | |||
| q2l1 |  Maribor | 4-1 | Željezničar | |||
| q2l1 |  AEL | 3-0 | Linfield | |||
| q2l1 |  BATE | 3-2 | Vardar | |||
| q2l1 |  Budućnost | 0-2 | Śląsk Wrocław | |||
| q2l1 |  Ludogorets | 1-1 | Dinamo Zagreb | |||
| Tuesday, 24 July 2012 | ||||||
| q2l2 | FC Salzburg | 4-3 | F91 Düdelingen | 4-4 | ||
| q2l2 | KR | 1-2 | HJK | 1-9 | ||
| q2l2 | Partizan | 3-1 | Valletta | 7-2 | ||
| q2l2 | Debrecen | 3-0 | Skënderbeu | 3-1 | ||
| q2l2 | FC Basel | 3-0 | Flora | 5-0 | ||
| q2l2 | Željezničar | 1-2 | Maribor | 2-6 | ||
| q2l2 | Sheriff | 1-0 | Ulysses | 2-0 | ||
| q2l2 | Ekranas | 2-1 | Shamrock Rovers | 2-1 | ||
| q2l2 | JFK Ventspils | 1-1 | Molde | 1-4 | ||
| q2l2 | Hapoel Ironi Kiryat Shmona | 2-0 | MŠK Žilina | 2-1 | ||
| q2l2 | Zestafoni | 2-2 | Neftçi | 2-5 | ||
| q2l2 | Shakhter | 1-1 | Slovan Liberec | 1-2, aet | ||
| Wednesday, 25 July 2012 | ||||||
| q2l2 | Dinamo Zagreb | 3-2 | Ludogorets | 4-3 | ||
| q2l2 | Linfield | 0-0 | AEL | 0-3 | ||
| q2l2 | Vardar | 0-0 | BATE | 2-3 | ||
| q2l2 | Helsingborg | 3-0 | The New Saints | 3-0 | ||
| q2l2 | Śląsk Wrocław | 0-1 | Budućnost | 2-1 | ||
