This paper proposed the different areas of improving cacao ecology that need to gain attention in the Philippines to augment the measures being undertaken to boost the country’s cacao plantations. This includes more research on areas of soil physicochemical properties, AMF genetic and functional diversity in cacao communities, and resistance to diseases of AMF-associated cacao trees. Appropriate application of AMF could increase the overall yield of the country’s cacao plantations and can be translated to improving food security and many other economic gains.