Due to the need for rural electrification, recent studies on the optimization of HRES has been conducted extensively to improve the planning process before microgrid implementation. Improvement in recent literature and practice have enabled new systems of storage to store energies as chemicals that would not be affected by the self-discharge rate, among others, of battery energy systems, albeit having its own disadvantages. Hence, this paper seeks to determine the applicability of an HRES system to consider these two types of storages and how a choice between the two can be made. With this goal, a mixed-integer linear programming model was formulated that aims to minimize the economic costs of an HRES microgrid implementation of a SPV/WTG/diesel system with battery and ammonia storage systems. The model would identify the number of each component to be installed as well as their sizes for SPV and WTG, being area and height, respectively. Since ammonia is a chemical that can be sold as fertilizer or fuel to bolster the economic viability of the system, the amount of energy needed to produce this chemical and to be sold was also determined. Moreover, the distribution of electricity from each source towards the demand loads would be determined to yield insights on the amount and proportion of energies generated, stored, and used throughout the planning horizon. Through this model, this paper has successfully formulated a model that provides decision support on several possible configurations of HRES microgrids to aid in its future developments.