National level approaches to the development and implementation of effective conservation policy and practice are often challenged by limited capacity and resources. Developing relevant and achievable priorities at the national level is a crucial step for effective conservation. The Philippine archipelago includes over 7000 islands and is one of only two countries considered both a global biodiversity hotspot and a megadiversity country. Yet, few studies have conducted overarching synthesis for threats and conservation priorities of any species group. As bats make up a significant proportion of mammalian diversity in the Philippines and fulfil vital roles to maintain ecosystem health and services we focus on assessing the threats and priorities to their conservation across the Philippines. Habitat loss from logging and agriculture and hunting are the main threatening process to over half of the Philippine bats. Using available information on species’ threats, conservation status, and endemism, we developed priority settings for Philippines bats to enable effective future decision making. We determined endemic and threatened species are the highest priority and larger bats are under more intense threat than smaller bats. Our finding further suggests that in order to bolster bat conservation and prevent future species loss, it is important to identify emerging threats and its extent, increase conservation education, develop effective policies, and forge equitable partnerships between scientists and stakeholders towards research and outreach capacity.