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| 1st(1st leg) | FC Flora | - | Lincoln Red Imps | 2:1 (1:0) | ||
| 2nd (2nd leg) | Lincoln Red Imps | - | FC Flora | 2:0 (1:0) | ||
| 1st(1st leg): 28/06/2016 17:00 | 2nd (2nd leg): 06/07/2016 18:00 | Winner: Lincoln Red Imps | ||||
| 1st(1st leg) | Valletta FC | - | B36 Tórshavn | 1:0 (0:0) | ||
| 2nd (2nd leg) | B36 Tórshavn | - | Valletta FC | 2:1 (1:1) | ||
| 1st(1st leg): 28/06/2016 18:00 | 2nd (2nd leg): 05/07/2016 18:00 | Winner: Valletta FC | ||||
| 1st(1st leg) | The New Saints | - | SP Tre Penne | 2:1 (2:1) | ||
| 2nd (2nd leg) | SP Tre Penne | - | The New Saints | 0:3 (0:1) | ||
| 1st(1st leg): 28/06/2016 19:00 | 2nd (2nd leg): 05/07/2016 19:30 | Winner: The New Saints | ||||
| 1st(1st leg) | FC Santa Coloma | - | FC Alashkert | 0:0 (0:0) | ||
| 2nd (2nd leg) | FC Alashkert | - | FC Santa Coloma | 3:0 (1:0) | ||
| 1st(1st leg): 28/06/2016 19:00 | 2nd (2nd leg): 05/07/2016 16:00 | Winner: FC Alashkert | ||||
