The western Amazon is characterized by a shortage of available minerals. Chemical analysis of food items and feces of frugivorous bats has shown that they may experience inadequate mineral intake. Assessing the inter-taxon and seasonal variations in mineral loads of wild frugivorous bats may help determine the mineral constraints in their diets. Our sampling was based on bats from the genus Carollia (n = 19 specimens) and the tribe Stenodermatini (n = 20; mainly genera Platyrrhinus and Artibeus) from highland tropical forests in Peru collected during the dry and wet seasons throughout a year. We analyzed the total concentrations of eight minerals in combined samples of liver and spleen for each bat, and compared concentrations between taxa and seasons. Our findings regarding manganese, iron, copper, zinc, and magnesium concentrations were generally consistent with those reported in the literature, while the sodium, potassium, and calcium concentrations would be the first reported in bats. We observed higher mineral concentrations in Carollia than in Stenodermatini bats, which may be linked with differences in their dietary preferences and inherent physiological characteristics. Seasonal mineral variations of frugivorous bats reported here were associated with temporal differences in the food items consumed and availability of mineral licks. Given that bats we studied come from a mineral-limited ecosystem, we suggest that Stenodermatini bats may face greater dietary limitations for sodium and potassium, and that frugivorous bats may exhibit seasonal constraints for copper and calcium. Recognition of potentially limited minerals, coupled with future studies on plant products that contain them, would be useful in the restoration programs for highland forests, which is one of the most threatened ecosystems in the Neotropics.