Fungal biotechnology is a rapidly advancing field that addresses critical global challenges in food security, energy, health, and environmental sustainability. This chapter provides a comprehensive overview of fungal biotechnology in the Philippines, spanning its historical roots, contemporary applications, and future directions. Indigenous practices such as the fermentation of rice wine (tapuy) and traditional food products highlight the country’s long-standing engagement with fungal processes. Modern research initiatives by different institutions in the Philippines have yielded notable innovations, including Trichoderma-based biofertilizers (e.g., BioQuick and BioGreen), mycorrhizal inoculants (e.g., Mykovam and VAMRI), and biocontrol agents targeting plant pathogens and nematodes. Advances in mushroom cultivation, production of single-cell proteins, and applications of fungal enzymes (amylases, lipases, proteases, cellulases, and pectinases) in the food industry underscore fungi’s economic value. Yeast biotechnology also holds significant promise, with yeasts such as Pseudozyma antarctica demonstrating potential in producing glycoproteins, recombinant proteins, and mannosylerythritol lipids with industrial and pharmaceutical applications. Environmental applications—including mycoremediation of heavy metals, dye decolorization, and bioenergy production through oleaginous yeasts and bioethanol—further illustrate the breadth of fungal biotechnology in the country. Despite these achievements, challenges persist in terms of funding, infrastructure, regulatory frameworks, and public awareness. There is a pressing need for expanded bioprospecting, strengthened biological resource centers, and interdisciplinary collaborations to harness the country’s rich fungal diversity for sustainable development. Strategic alignment with national priorities and the UN Sustainable Development Goals will ensure that Philippine fungal biotechnology continues to grow as a driver of innovation in agriculture, health, and environmental stewardship in the ASEAN region.