This work investigates the viability of fuel cells (FC) as combined heat and power (CHP) prime movers in commercial buildings with a specific focus on supermarkets. Up-to-date technical data from a FC manufacturing company was obtained and applied to evaluate their viability in an existing food-retail building. A detailed optimisation model for enhancing distributed energy system management described in previous work is expanded upon to optimise the techno-economic performance of FC-CHP systems. The optimisations employ comprehensive techno-economic datasets that reflect current market trends. Outputs highlight the key factors influencing the economics of FC-CHP projects. Furthermore, a comparative analysis against a competing internal combustion engine (ICE) CHP system is performed to understand the relative techno-economic characterisitcs of each system. Results indicate that FCs are becoming financially competitive although ICEs are still a more attractive option. For supermarkets, the payback period for installing a FC system is 4.7–5.9 years vs. 4.0–5.6 years for ICEs when policies are considered. If incentives are removed, FC-CHP systems have paybacks in the range 6–10 years vs. 5–8.5 years for ICE-based systems. A sensitivity analysis under different market and policy scenarios is performed, offering insights into the performance gap fuel cells face before becoming more competitive.