Bats provide important ecosystem services for agriculture, such as pest control, a function that is particularly relevant for small-scale farmers. However, climate change is causing a decrease in bat populations. To assess the potential impacts of climate change on insectivorous bats and the implications on small-scale farming of indigenous communities in the Chiapas Highlands in southern Mexico we developed a three-step protocol: (1) projecting distribution shifts of insectivorous bats under climate change scenarios using non-dispersal and limited-full dispersal assumptions, (2) using official information to estimate the average economic value of conducting chemical pest control in crops at a state level, (3) surveying small-scale farmers to estimate the local economic value of pest control and determine how bats are perceived by small-scale farmers. Our models project shifts in bat species due to climate change. Given that new suitable climatic areas are also projected, if we assume a limited-full dispersal scenario, bats might not be as at risk by climate change, but shifting their distribution to more suitable habitats will probably affect the dynamic of the ecosystem service they provide. The official estimated value of chemical pest control is $15.15 USD/ha, while the estimated cost resulting from a hybrid survey with small-scale farmers was $47.53 USD/ha. The difference in cost could be related to an overuse of insecticides for pest control or an increase in price due to reduced accessibility. Sixty percent of surveyed farmers perceived a decline in bat populations, 68% were unaware of the benefits that bats provide to their crops, 51% believe that bats are mainly hematophagous, and 10% recognize that people harm or kill bats. A new approach including communicating small-scale farmers in their native languages the benefits that insectivorous bats provide along with a pest management strategy for the efficient use of insecticides needs to be implemented.