Natural habitats have drastically regressed due to rapid changes in land‐use during recent decades, generating a decrease in species diversity. In light of natural habitat destruction worldwide, there is a need to adopt an integrative approach to the study of biodiversity in order to better assess the magnitude of diversity loss in landscapes affected by human intervention. The aim of this study was to assess and compare anuran assemblages under different land‐uses in a subtropical forest of NW Argentina using an integrative view of diversity through different measures. We assessed alpha and beta diversity components for three complementary diversity measures: species richness, functional diversity and phylogenetic diversity in three land‐uses: forest, tobacco and suburban. We carried out generalized linear mixed models with an autocorrelation structure to compare the three diversity measures across the different land‐uses. We also used a beta diversity partitioning method to determine nestedness and turnover processes in taxonomic, functional and phylogenetic dissimilarity. Our results suggest a filtering effect of the land‐uses on the diversity of anuran assemblages in the surveyed area, with an increased loss of anuran diversity in areas with intensified land‐use, such as tobacco monoculture. This study contributes to understand amphibian communities associated to modified habitats in the Southern Andean Yungas forests from Argentina. Our findings highlight the importance of disentangling each diversity component separately to detect more accurately the diversity patterns associated to land‐use change.