The role of sustainable nature-based tourism (also called ecotourism) in conserving biodiversity is paramount given that tourism and nature are intricately linked. The Philippines, by virtue of its ratification of the Convention on Biological Diversity, has a legal obligation to halt biodiversity loss. One of the conservation measures that has been suggested, as being pragmatic and effective in pursuing this conservation commitment, is sustainable nature-based tourism. This paper has two parts. Part I explores the role of ecotourism in conserving biodiversity within protected areas in the Philippines; it also discusses nature-based tourism practices and policies in natural destinations in the country. Part II outlines the various ways by which ecotourism can contribute to meeting the main goal of the Convention on Biological Diversity, particularly, the Aichi Biodiversity Targets. The main issues and challenges confronting the Philippine government and other relevant stakeholders with regard to the integration of ecotourism and biodiversity conservation are also presented. This paper can be useful to other countries that have similar issues and concerns.