Cave guano derived from insectivorous bats and birds contain unique geochemical and mineralogical signatures. We investigated the mineralogy, pH, C, N and metal abundance patterns of cave guano spatially and temporally (with depth) along a W-E transect in Malaysia and Palawan from five remote cave sites, each housing large populations of bats and Aerodramus spp.(cave swiftlets). Guano deposits were rich in phosphate and/or sulphate minerals (e.g., gypsum, bassanite) with leucophosphite, spheniscidite, and variscite present in most profiles. Metal abundances measured from modern and ancient bat guano revealed high concentrations of transition metals relative to the local environment. Highly enriched metals, however, were associated with phosphate rather than sulphate minerals. Copper and Zn were enriched in all profiles, whereas other metals were associated with specific caves consistent with known local mineral resources. For example, Sn, Pb, and Rb were particularly enriched in Batu Cave, located in the Peninsular Malaysian granitic tin belt, whereas Ni and Cr were high in regions associated with ultramafic ophiolites and Ni-laterites found on Palawan.