Through the integration of multiple energy carriers with related technologies, multi-energy systems (MES) can exploit the synergies coming from their interplay for several benefits towards decarbonization. In such a context, inclusion of Power-to-X technologies in periods of excess renewable electricity supply, removes the need for curtailment of renewable electricity generation. In order to achieve the environmental benefits of MES without neglecting their economic feasibility, the optimal design problem is as crucial as challenging and requires the adoption of a multi-objective approach. This paper extends the results of a previous work, by investigating hydrogen-based non-conventional storage for PV power in the eco-energetic optimization of an MES. The system under study consists of a reversible fuel cell (r-SOC), photovoltaic (PV), electric heat pump, absorption chiller and thermal storage, and allows satisfying the multi-energy needs of a residential end-user. A multi-objective linear problem is established to find the optimal MES configuration including the sizes of the involved technologies with the goal of reducing the total annual cost and the fossil primary energy input. Simulation results are compared with those obtained in previous work with a conventional nanogrid where a combined heat and power (CHP) system with gas-fired internal combustion engine and a battery were present instead of an r-SOC. The optimized configuration of the non-conventional nanogrid allows achieving a maximum primary energy reduction amounting to 66.3%, compared to the conventional nanogrid. In the face of the environmental benefits, the non-conventional nanogrid leads to an increase in total annual costs, which, compared to the conventional nanogrid, is in the range of 41–65%.