Deforestation, agricultural intensification, and habitat homogenization are critical threats to biodiversity in Southeast Asia. Limited information is available on the trophic and physiological responses of tropical animals to these environmental changes. The wrinkle-lipped free-tailed bat Chaerephon plicatus is a cave roosting species that is experiencing population declines across Southeast Asia, where landscapes have been drastically modified. In our study site in central Thailand, we tested the hypothesis that wrinkle-lipped free-tailed bats living in landscapes that contrast in heterogeneity and land-use differed in mercury contamination, trophic position and physio-immunological status. Bats from less heterogeneous landscapes (dominated by rice crops, absence of large forest patches) occupied a lower trophic position than conspecifics from more heterogeneous landscapes (including large forest patches). Additionally, bats from these habitats had lower concentrations of mercury in erythrocytes, lower body mass, higher antioxidant superoxide dismutase (SOD), lower antioxidant glutathione peroxidase (GPx) and lower values of the GPx/SOD ratio than bats from more heterogeneous landscapes. Individual bat mercury concentrations were positively correlated with body mass and two immune markers (lysozyme and immunoglobulin) but were negatively correlated with plasma non-enzymatic antioxidant capacity. Our results suggest various links between landscape heterogeneity, mercury accumulation/exposure, and health status of wildlife in Southeast Asian countries.