Sustainable energy management becomes more important due to the ever more actual problems of environmental pollution and limited natural resources. The fuel cell technology is one of the most attractive solutions in this sense. During the past decades fuel cells have been investigated and demonstrated for several applications. One of the most attractive applications is using fuel cell system for stationary energy cogeneration (CHP), since they are capable of producing thermal energy and power with higher efficiencies and in a more environmentally friendly way than most of the conventional commercial techniques. The purpose of this work is to investigate the feasibility of integrating a PEMFC system with a commercial greenhouse and to assess the mutual benefits deriving from this integration. The main task of this connection is to recover the low temperature wasted heat delivered by the PEMFC system and by the fuel reforming process in order to meet the thermal energy demand of a commercial greenhouse. In this study an energy analysis was performed in order to evaluate the energetic performance of the system. To achieve this aim, first, a model of the whole system was developed in TRNSYS environment. In addition to the aforesaid, a sensitivity analysis was also carried out varying the main influencing operating parameters in order to evaluate an optimal configuration of the system. Considering a commercial greenhouse’s usual thermal and electrical demand, the results shows that by integrating a 3 KW fuel cell system, able to cover approximately the 25% of the electricity requested during the year, and taking into account both heat recovery from the fuel cell system and the ones from the fuel reforming, roughly 30% of the heating demand of a 1000 m2 commercial greenhouse can be supplied.