| Date | Phase | Home | Away | |||
|---|---|---|---|---|---|---|
| 23/01/2013 | Fourth round | Balzan | | 3-2 | | Gzira |
| 23/01/2013 | Fourth round | Sannat Lions F.C. | | 0-5 | | Rabat Ajax |
| 23/01/2013 | Fourth round | Qormi | | 2-1 | | Birkirkara |
| 23/01/2013 | Fourth round | Lija | | 1-0 | | Floriana |
| 17/02/2013 | Quarter-finals | Rabat Ajax | | 0-3 | | Valletta |
| 17/02/2013 | Quarter-finals | Hibernians | | 3-0 | | Zebbug Rangers |
| 17/02/2013 | Quarter-finals | Balzan | | 0-1 | | Qormi |
| 17/02/2013 | Quarter-finals | Saint Andrew's | | 0-1 | | Lija |
| 17/05/2013 | Semi-finals | Qormi | | 1-0 | | Lija |
| 18/05/2013 | Semi-finals | Valletta | | 2-3 | | Hibernians |