A system and method for breaking-in and humidifying membrane-electrode-assemblies (MEAs) in a fuel cell stack. The method includes performing voltage cycling and humidification of the MEAs in the stack, including one or more temperature steps wherein current density of the stack is cycled within a predetermined range for each of the one or more temperature steps. The method also includes maintaining a fuel cell stack voltage within a predetermined range, and maintaining anode and cathode reactant flows at an approximate set-point during the current density cycling of the one or more temperature steps to break-in and humidify the MEAs in the stack so that the stack is able to operate at a predetermined threshold for a fuel cell stack voltage output capability.