The building sector is one of the key energy consumers worldwide. Fuel cell micro-Cogeneration Heat and Power systems for residential and small commercial applications are proposed as one of the most promising innovations contributing to the transition towards a sustainable energy infrastructure. For the application and the diffusion of these systems, in addition to their environmental performance, it is necessary, however, to evaluate their economic feasibility. In this paper a life cycle assessment of a fuel cell/photovoltaic hybrid micro-cogeneration heat and power system for a residential building is integrated with a detailed economic analysis. Financial indicators (net present cost and payback time are used for studying two different investments: reversible-Solid Oxide Fuel Cell and natural gas SOFC in comparison to a base scenario, using a homeowner perspective approach. Moreover, two alternative incentives scenarios are analysed and applied: net metering and self-consumers’ groups (or energy communities). Results show that both systems obtain annual savings, but their high capital costs still would make the investments not profitable. However, the natural gas Solide Oxide Fuel Cell with the net metering incentive is the best scenario among all. On the contrary, the reversible-Solid Oxide Fuel Cell maximizes its economic performance only when the self-consumers’ groups incentive is applied. For a complete life cycle cost analysis, environmental impacts are monetized using three different monetization methods with the aim to internalize (considering them into direct cost) the externalities (environmental costs). If externalities are considered as an effective cost, the natural gas Solide Oxide Fuel Cell system increases its saving because its environmental impact is lower than in the base case one, while the reversible-Solid Oxide Fuel Cell system reduces it.