Proton exchange membrane fuel cell (PEMFC) is regarded as a potential future power technology for stationary and mobile applications due to its high efficiency (full and partial load), rapid start‐up, high power density, and low emissions.Depending on their particular application field (decentralized combined heat and power production, uninterrupted power supplies (UPS), or mobile applications) different operating conditions and designing parameters are required and different performance can be expected.Thus, the aim of this paper is to investigate the behavior and performance of two stacks of the same size, developed with a different approach according to their application sectors.The first PEMFC stack is designed for UPS units or mobile purpose, the second one, is designed to supply heat and power in residential applications (CHP units).The analysis of the stacks behavior has been carried out by using both experimental and numerical investigations.Experimental results have allowed: (i) to characterize the stacks; (ii) to calibrate the numerical model; (iii) to supply useful data for setting and improving the control system.