An electrochemical system having an electrochemical compressor with an operating voltage that is controlled by a controller is described. The operating voltage between a first and second electrodes separated by an ion conducting material, such as a proton conducting polymer, may be oscillated in a waveform. The controller may reduce the voltage to low pressure side of the electrochemical compressor to initiate electrolysis for a set time interval and then may change the operating voltage to operate the electrochemical cell in a compressor mode. When the electrochemical cell is operating in an electrolysis mode, in situ hydrogen is produced on the low pressure side that may be used as a electrochemically active component of the working fluid when the electrochemical cell is switched to a compressor mode. The controller may have a control program that automatically controls the operating waveform as a function of sensor input.