Combined heat and power (CHP) systems are a proven technology to reduce emissions. A methodology was presented to compare the economic feasibility of fuel cell-based CHP systems with more alternative prime movers (microturbine and gas turbine). For demonstration purposes, the methodology was applied to three distinct case studies of varying size. The developed methodology allowed for the analysis of the system from various economic points of view. Because of the scarcity of complete equation sets modeling the off-design performance of fuel cells, several novel equations were proposed. All systems utilizing alternative prime movers were unprofitable. The fuel cell-based systems exhibited some economic potential; however, the results showed it would take close to the entire system lifetime to recover the capital costs. This is consistent with the reviewed literature and hence validates the new methodology and partial load equations proposed. Based on this analysis the fuel cell-based system for the medium sized case study showed the most economic potential. Because of the susceptibility of emerging technologies (fuel cells) to changes in capital costs, an in-depth sensitivity analysis was performed. The analysis showed that a 5% decrease in capital costs could reduce the payback period by as much as six months. This indicates that only a small decrease in price is necessary to potentially lead to the adoption of these systems in the near future.