Flying foxes of the genus Pteropus are predominantly island taxa, with high levels of endemism, and face high risks of extinction. Their ecological and economic importance in island ecosystems has been widely recognized. Here we investigate the population size and conservation status of the Vulnerable Pteropus voeltzkowi, endemic to the western Indian Ocean island of Pemba, Tanzania. Direct counts and patch counts were used to determine abundance of flying foxes at roost sites, supplemented with evening dispersal counts, which were conducted to test accuracy of counting techniques under varying conditions of visibility. We estimate that the population size is now a minimum of 18,200–22,100, thus validating reports of annual increases by in-country monitoring teams since the last documented population survey of 4,600–5,500 bats in 1995. Taking into account differences in the counting methodologies for roosting bats we estimate that the population size could be as high as 35,600 individuals. We identified 44 occupied roosting sites, with just four of these supporting up to 87% of the population. Roost disturbance represents a continuing threat to this species and was found to influence roost occupancy and colony size. The implications of the population increase for the local human community are discussed and recommendations provided for continued monitoring and future management of this species on Pemba Island.