A system and method is disclosed for managing the access to GPIO ports that are coupled to input pins of devices in the computer system. Access commands directed to a GPIO port are monitored. When an access command is detected, an interrupt is issued and an interrupt handler determines if the access command is authorized. If the command is authorized, the interrupt handler completes the access command and returns control to the software program that issued the access command. If the command is not authorized, the command is prevented from reaching the GPIO and the access attempt is logged. The GPIO ports that are monitored may be those GPIO ports that are coupled to an input or enable pin of a sensitive hardware component within the computer system.