Over the last years, many studies focused on the development of membrane reactors for micro-cogeneration systems based on PEM fuel cells, thanks to its unique feature of separating pure hydrogen. This work deals with (i) the design of a fluidized bed membrane reactor flexible towards different natural gas (NG) qualities and (ii) its integration in PEM based systems of 5 kW power output. Four typical NG compositions from reference European countries have been identified in this study featuring an average condition and three extreme cases. Two different membrane reactor models were developed: a 1D phenomenological model and a quasi-lumped model inside the overall system implemented in Aspen Plus. Results show the importance of taking into account the natural gas composition in the design phase: only assuming the NG with the highest inert content as base case, the target electric efficiency of 39% can be reached for any other case.