Despite their critical role as reservoir hosts for many zoonotic diseases, the impact of land-use and land-cover changes (LCLUC) on flying foxes' interactions with humans remains unclear, posing a potential public health risk. To address this, we apply optimal foraging theory and individual-based modelling to simulate flying-fox movement and population dynamics under various LCLUC scenarios. After validating our model against available data, we analyze the effects of agriculturalization, urbanization, forest fragmentation, and reforestation on flying-fox densities across synthetic landscapes of urban, forest, orchard, and water-body habitats. Our findings indicate that habitat disruption—particularly fragmentation through urbanization—significantly increases the risk of zoonotic spillover events by increasing contacts between species. Scenarios of forest degradation reveal that ecologically degraded forest environments can further exacerbate this risk. Additionally, we find that reforestation can alleviate spillover risk. These results underscore the importance of conservation and habitat restoration as critical strategies for mitigating zoonotic disease transmission.