| 3. Round | 12/09/2016 | Rayo OKC | - | Jacksonville Armada | 3:2 | ||||
| 3. Round | 18/09/2016 | Puerto Rico FC | - | Jacksonville Armada | 3:3 | ||||
| 3. Round | 29/09/2016 | Jacksonville Armada | - | FC Edmonton | 0:0 | ||||
| 4. Round | 02/10/2016 | Minnesota United FC | - | Jacksonville Armada | 0:1 | ||||
| 4. Round | 13/10/2016 | Jacksonville Armada | - | Indy Eleven | 0:0 | ||||
| 4. Round | 16/10/2016 | Jacksonville Armada | - | New York Cosmos | 2:4 |  |
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| 4. Round | 23/10/2016 | FC Edmonton | - | Jacksonville Armada | 1:0 | ||||
| 4. Round | 30/10/2016 | Jacksonville Armada | - | Tampa Bay Rowdies | 3:2 |
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