Large seed dispersers play a key role in maintaining and restoring tree species diversity in tropical forests. These taxa may also represent important food sources for sympatric carnivores. Therefore, their occurrence and population status have implications for the health of the forest and conservation of predators. Here we examined patterns of occurrence of pig-tailed macaques (Macaca nemestrina), bearded pigs (Sus barbatus), muntjac deer (Muntiacus spp.), mouse deer (Tragulus spp.) and sambar deer (Rusa unicolor) across study areas on Indonesian Borneo characterised by different land use histories and forest changes. We expected that human activities, including logging and hunting, would have a negative effect on mean occupancy of these taxa. We also predicted that the relative abundance of Sunda clouded leopard (Neofelis diardi) would affect prey activity patterns. We conducted systematic camera trap surveys across six study areas on Indonesian Borneo and analysed data using occupancy modelling. Overall, mean occupancy probabilities for the clouded leopard’s prey species within regenerating forests were comparable to those in pristine habitats, but severely decreased at a site with ongoing human disturbance (logging and hunting). Mouse deer and muntjac deer diurnal activity positively correlated with detection rates of clouded leopards across sites, whereas other prey taxa showed no significant relationship. Therefore, some taxa are able to recolonise regenerating forests relatively quickly, but their distribution is reduced when simultaneous logging and hunting occur. In addition, mouse deer and muntjac deer appear able to adjust their activity patterns in response to the risk of predation. Our results provide support for investing conservation efforts of regenerating forests on Indonesian Borneo, which benefits the conservation of important large seed dispersers including primates and ungulates. Maintaining populations of large prey taxa will be crucial for the long-term persistence of clouded leopards.