The expansion of the agricultural frontier in the species-rich tropical regions of the world has generated conflicts between the need to secure food production and the conservation of biodiversity. As natural areas give way to farmlands, the future of sensitive taxa may depend on how intensively the crops are cultivated. In order to better understand the response of avian diversity to cultivation intensity in tropical farmlands, analyses of species richness are increasingly being complemented with information about the birds’ functional roles and evolutionary history. In this study, we analysed the association of several features of vegetation composition and structure, as indicators of cultivation intensity in coffee farms in Costa Rica, on the taxonomic, functional and phylogenetic dimensions of avian biodiversity at the local scale across an approximately 2000 m elevational gradient. Bird detections and vegetation measurements were conducted at 120 randomly selected circular plots of 25 m radius, across 51 coffee farms. Using regression modelling and multi-model inference, we related six vegetation features to five biodiversity metrics in this system and evaluated whether the results differed among elevational zones. The most influential vegetation feature was the number of trees with a diameter-at-breast-height larger than 30 cm, promoting higher richness, functional redundancy and phylogenetic structure of avian species. Shade from canopy cover and the number of non-coffee crops increased species and phylogenetic richness, respectively. The effect of individual vegetation features on particular biodiversity metrics varied across elevation, possibly due to the idiosyncratic response of each dimension to the elevation gradient or because of local ecological processes. We conclude that vegetation features related to cultivation intensity have effects on avian diversity, but that these effects differ among biodiversity metrics and are sensitive to the environmental context. Consequently, targeted conservation management should be based on more comprehensive studies that include more than one biodiversity dimensions as well as variation in relevant environmental context. In general, our results suggest that, when designing conservation strategies for birds in coffee-dominated landscapes, there is likely no “one-size-fits-all” strategy.