This paper presents an economic impact analysis and carbon footprint study of a hydrogen-based microgrid. The economic impact is evaluated with respect to investment costs, operation and maintenance (O&M) costs, as well as savings, taking into account two different energy management strategies (EMSs): a hydrogen-based priority strategy and a battery-based priority strategy. The research was carried out in a real microgrid located at the University of Huelva, in southwestern Spain. The results (which can be extrapolated to microgrids with a similar architecture) show that, although both strategies have the same initial investment costs (EUR 52,339.78), at the end of the microgrid lifespan, the hydrogen-based strategy requires higher replacement costs (EUR 74,177.4 vs. 17,537.88) and operation and maintenance costs (EUR 35,254.03 vs. 34,877.08), however, it provides better annual savings (EUR 36,753.05 vs. 36,282.58) and a lower carbon footprint (98.15% vs. 95.73% CO2 savings) than the battery-based strategy. Furthermore, in a scenario where CO2 emission prices are increasing, the hydrogen-based strategy will bring even higher annual cost savings in the coming years.