This study consists on online detection of fuel cell dysfunction in embedded applications without additional hardware component. The power converter usually coupled with the fuel cell is used to perform the diagnosis strategy. The main interest of the method presented in this paper is to simultaneously optimize the performances, the cost and the size of the Proton Exchange Membrane Fuel Cell (PEMFC). In this work, we focus on a system including a fuel cell stack coupled with an isolated DC/DC power converter and controlled by a Digital Signal Processor (DSP). These elements associated with measurement sensors and adequate programmings allow the control of the power conversion and the determination of fuel cell health at the same time. The fuel cell harmonic impedance is measured using spectroscopy method for a large frequency range. Specific cases of fault detections related to membrane humidification and reactive gas feeding are treated in this paper.