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Insectivorous bats populate habitats that adjoin or overlap with agricultural lands, and tend to use cultivated land for foraging and commuting. The goal of the study was to assess the principal factors influencing the activity and species richness of insectivorous bats in a semi-arid Mediterranean agroecosystem. We hypothesized that bat activity and species richness are influenced by the anthropogenic factors that are typical of agroecosystems, such as fragmentation of the landscape and loss of natural habitat, agrochemical use, presence of powerlines and roads, and proximity to urban areas. We recorded bats in a diversified semi-arid Mediterranean agroecosystem in 2012 and 2013 and estimated the effect of various anthropogenic and environmental factors on their activity. The proportion of natural and semi-natural habitats at the landscape and at the plot scale were the most important predictors of total bat activity, and of the activity the two most common species recorded, Pipistrellus kuhlii and Tadarida teniotis, both known to be synanthropic. Indeed, P. kuhlii had a positive association with the proximity to bodies of water and to settlements. Total bat activity was negatively associated with the use of agrochemicals. Thus, in line with our predictions, both the proportion of natural land cover in the environment and the use of agrochemicals play an important role in determining bat distribution in agricultural environments. Ecological inferences based on our results can be used to develop management schemes, such as restoring patches of natural vegetation near and within farmlands, to increase the suitability of agroecosystems as habitats for insectivorous bats. These could contribute both to the protection of endangered bat species and to bio-control of insect pests.