| 1. Jornada | 18.01.2009 | CF Monterrey | - | Puebla FC | 4:0 | ||||
| 2. Jornada | 25.01.2009 | Puebla FC | - | Club Necaxa | 1:0 | ||||
| 3. Jornada | 01.02.2009 | Santos Laguna | - | Puebla FC | 0:0 | ||||
| 4. Jornada | 08.02.2009 | Puebla FC | - | Deportivo Toluca | 0:2 | ||||
| 6. Jornada | 19.02.2009 | Puebla FC | - | CF Pachuca | 2:2 |  |
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| 7. Jornada | 22.02.2009 | Jaguares Chiapas | - | Puebla FC | 2:4 | |
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| 8. Jornada | 01.03.2009 | Puebla FC | - | Atlas Guadalajara | 1:1 | ||||
| 9. Jornada | 08.03.2009 | UANL Tigres | - | Puebla FC | 1:2 | ||||
| 10. Jornada | 15.03.2009 | Puebla FC | - | Club San Luis | 2:1 | |
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| 11. Jornada | 22.03.2009 | Atlante | - | Puebla FC | 0:1 | ||||
| 12. Jornada | 05.04.2009 | Puebla FC | - | CF América | 2:3 | ||||
| 13. Jornada | 12.04.2009 | Pumas UNAM | - | Puebla FC | 3:1 |  |
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| 14. Jornada | 19.04.2009 | Cruz Azul | - | Puebla FC | 1:2 | |
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| 15. Jornada | 26.04.2009 | Puebla FC | - | Indios Juárez | 0:2 | ||||
| 16. Jornada | 03.05.2009 | Deportivo Guadalajara | - | Puebla FC | 0:0 | ||||
| 17. Jornada | 10.05.2009 | Puebla FC | - | UAG Tecos | 1:1 | |
Honduras