Agricultural landscapes worldwide are heavily sprayed with agrochemicals to increase crop productivity. These agrochemicals release bio-accumulative pollutants such as heavy metals that often persist in the environment with harmful impacts on biota. In a prime endangered Atlantic Forest biome, in Bahia, Brazil, agroforestry of cacao (
Theobroma cacao
) provides a livelihood for small farmers and suitable habitats for forest species. However, landscape transformation to pasture and monoculture expose vulnerable communities to scarcely evaluated pollutants with unknown effects on the health of humans and animals. We assessed the bioaccumulation of manganese (Mn), lead (Pb), and copper (Cu) by analyzing hair samples of 326 bats representing 28 species across 15 cacao agroforestry and 2 forest remnants. Bats from regions heavily disturbed by pastures and monocultures showed higher levels of Pb (41.20 µg/g) and Mn (0.44 µg/g) compared to those from areas where forest or cacao agroforestry dominates the landscape. Local grassland covers increased Pb bioaccumulation, while forest cover reduced it. Cacao agroforestry appeared to increase Cu exposure, likely due to fungicide use. This study pioneers the evaluation of heavy metal accumulation in bats inhabiting cacao agroforestry and Atlantic Forest remnants, highlighting the need for sustainable agricultural practices to protect wildlife and ecosystem health.