Hybrid microgrids, integrating renewable energy sources and energy storage, are key in extending energy access in the remote areas of developing countries, in a sustainably way and in providing a good quality of service. Their extensive development faces a financing gap, having a high capital expenditure (CAPEX) also due to high storage costs. In the present work, a case study of a Ugandan microgrid was used to compare various battery technologies employed on their own and in a combination with a flywheel, in terms of their durability and the overall levelized cost of energy (LCOE) of the plant. Simulations show how hybrid storage configurations result in a lower LCOE for the current load profile of the microgrid and even more so for two reference residential and industrial load scenarios, suggesting this would remain the best solution even accounting for future socio-economic development. The resulting LCOE for hybrid storage configurations is lower than the average values reported for microgrid projects and represents a promising solution to speed up the development of such electrification initiatives.