| 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, 12 July 2016 | ||||||
| q2l1 |  FC Salzburg | 1-0 | FK Liepāja | |||
| q2l1 |  Vardar | 1-2 | Dinamo Zagreb | |||
| q2l1 |  Dinamo Tbilisi | 2-0 | Alashkert | |||
| q2l1 |  BATE | 2-0 | Seinäjoen JK | |||
| q2l1 |  Valletta | 1-2 | Crvena Zvezda | |||
| q2l1 |  Qarabag | 2-0 | F91 Düdelingen | |||
| q2l1 |  The New Saints | 0-0 | APOEL | |||
| q2l1 |  Hapoel Beer Sheva | 3-2 | Sheriff | |||
| q2l1 |  Zrinjski | 1-1 | Legia Warszawa | |||
| q2l1 |  Lincoln Red Imps | 1-0 | Celtic | |||
| Wednesday, 13 July 2016 | ||||||
| q2l1 |  Rosenborg | 3-1 | IFK Norrköping | |||
| q2l1 |  Dundalk | 1-1 | FH | |||
| q2l1 |  Olimpija | 3-4 | AS Trenčín | |||
| q2l1 |  Žalgiris | 0-0 | Astana | |||
| q2l1 |  Partizani | 1-1 | Ferencváros | |||
| q2l1 |  Crusaders | 0-3 | FC København | |||
| q2l1 |  Ludogorets | 2-0 | OFK Titograd | |||
| Tuesday, 19 July 2016 | ||||||
| q2l2 | Legia Warszawa | 2-0 | Zrinjski | 3-1 | ||
| q2l2 | FC København | 6-0 | Crusaders | 9-0 | ||
| q2l2 | Crvena Zvezda | 2-1 | Valletta | 4-2 | ||
| q2l2 | APOEL | 3-0 | The New Saints | 3-0 | ||
| q2l2 | FK Liepāja | 0-2 | FC Salzburg | 0-3, aet | ||
| q2l2 | Sheriff | 0-0 | Hapoel Beer Sheva | 2-3 | ||
| q2l2 | Seinäjoen JK | 2-2 | BATE | 2-4 | ||
| q2l2 | OFK Titograd | 0-3 | Ludogorets | 0-5 | ||
| q2l2 | Alashkert | 1-1 | Dinamo Tbilisi | 1-3 | ||
| Wednesday, 20 July 2016 | ||||||
| q2l2 | Celtic | 3-0 | Lincoln Red Imps | 3-1 | ||
| q2l2 | IFK Norrköping | 3-2 | Rosenborg | 4-5 | ||
| q2l2 | Ferencváros | 1-1 | Partizani | 2-2, aet, p1-3 | ||
| q2l2 | Dinamo Zagreb | 3-2 | Vardar | 5-3 | ||
| q2l2 | FH | 2-2 | Dundalk | 3-3 | ||
| q2l2 | AS Trenčín | 2-3 | Olimpija | 6-6 | ||
| q2l2 | F91 Düdelingen | 1-1 | Qarabag | 1-3 | ||
| q2l2 | Astana | 2-1 | Žalgiris | 2-1 | ||
