Islands are ideal systems to reconstruct changes in biodiversity and reveal the influence of humans on natural communities. While theory predicts biodiversity on islands tends towards equilibrium, the recent extinction of large proportions of island biotas complicates testing this model. The well-preserved subfossil record of Caribbean bats provides a rare opportunity to model diversity dynamics in an insular community. Here we reconstruct the diversity trajectory in noctilionoid bats of the Greater Antilles by applying a dynamic model of colonisation, extinction and speciation to phylogenetic and paleontological data. We show species richness asymptotes to an equilibrium value, demonstrating natural equilibrium dynamics across an entire community. However, recent extinctions have wiped out nearly a third of island lineages, dragging diversity away from equilibrium. Using a metric to measure island biodiversity loss, we estimate it will take at least eight million years to regain pre-human diversity levels. Our integrative approach reveals how anthropogenic extinctions can drastically alter the natural trajectory of biological communities.