Abstract Bats are well known for playing an important role in several ecosystem services such as arthropod population control, insect pest suppression in agricultural systems and vector disease control, but also for acting as ecological indicators. Their population dynamics are strongly linked to environmental variations and, in some cases, reflect the health status of ecosystems. Hence, some species have an excellent potential as ecological indicators due to their sensitivity to ecosystem changes. Despite the general decrease of many bat populations worldwide and the recent upsurge in the use of autonomous acoustic detectors, the acoustic monitoring of bat assemblages is still an emerging field in bat research and conservation. Probably due to a general lack of methodological standards and the lack of common ecological indices, few long-term bat acoustic monitoring programs are currently active and data is rarely shared and compared between regions. In this study we propose and adapt a set of different ecological indices that can be used in acoustic surveys designed to detect changes in bat diversity, activity and assemblage composition, all of which can be linked to species’ climatic and habitat-related preferences. Using a dataset collected during three years of bat monitoring in Catalonia (NE Iberian Peninsula), we used three traditional indices (richness, activity and Shannon diversity) and developed four new ecological indices (Community Thermal Index, Community Precipitation Index, Community Openness Index and Community Specialization Index) that enabled us to study bat communities and compare them at different spatial and temporal scales. Here, we demonstrate the applicability of these indices in bat monitoring programs. We also provide a consistent tool for generating easy-to-interpret ecological indices when monitoring the short- and long-term responses of bats under the current scenario of global change. Using standardized protocols and robust ecological indices enables studies and datasets to be compared, which in turn promotes the development of proper management and conservation measures via international cooperation.