A controller-executed method for conditioning a membrane electrode assembly (MEA) in a fuel cell for use in a fuel cell stack includes humidifying a fuel inlet to the stack to a threshold relative humidity level, and maintaining a current density and cell voltage of the fuel cell at a calibrated current density level and hold voltage level, respectively, via the controller in at least one voltage recovery stage. The recovery stage has a predetermined voltage recovery duration. The method includes measuring the cell voltage after completing the predetermined voltage recovery duration, and executing a control action with respect to the fuel cell or fuel cell stack responsive to the measured cell voltage exceeding a target voltage, including recording a diagnostic code via the controller indicative of successful conditioning of the MEA. A fuel cell system includes the fuel cell stack and controller.