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The increasing expansion of monoculture plantations poses a major threat to Asian tropical biodiversity. Yet, in many countries such as the Philippines, the ability of species to persist within plantations has never been explored. We studied the seasonal activity and response of fruit bats in two types of monocultural plantations (rubber and oil palm) in the Southern Philippines from 2016–17 for 12 months. Our mist-netting and monitoring data showed that both plantations can support cosmopolitan species of fruit bats (Cynopterus brachyotis, Eonycteris spelaea, Macroglossus minimus, Ptenochirus jagori, and Rousettus amplexicaudatus), yet a significant variation in the abundance and guild distribution between plantations was observed. Rubber hosted a higher bat abundance than oil palm, which may be influenced by better habitat structure of the matrix (e.g., presence of orchard and fruit plantations) and practices occurring in the rubber plantation. We find that, among seasonal climatic variables, temperature showed significant negative effects on fruit bat abundance. Our results suggest that although monoculture plantations host low diversity (i.e., richness and endemism) they still support generalists which are still ecologically important species. Furthermore, wildlife-friendly commercial plantation practices could both enhance economic growth and biodiversity conservation in the Philippines. Our data both provide the potential for long-term monitoring in the Philippines and highlight the need for more comprehensive monitoring of other bat functional groups and their ability to transverse plantations to provide a more in-depth understanding of the roles and impacts of plantations and other land-use changes.