Method to automatically enable/disable stack reconditioning procedure based on fuel cell stack parameter estimation

A system and method for determining when to trigger reconditioning of a fuel cell stack and when to disable the reconditioning of the fuel cell stack. In one embodiment, the stack reconditioning is triggered when a maximum stack power estimation falls below a first predetermined power threshold. The reconditioning of the stack can be disabled so it is not performed when the trigger occurs if the reconditioning process does not raise the maximum power estimation above a second predetermined power threshold or the time from one reconditioning trigger to a next reconditioning trigger is less than a predetermined time threshold, or both.