AbstractUnderstanding the impacts of habitat conversion on species assemblages across multiple biodiversity dimensions (taxonomic, functional, and phylogenetic) and spatial scales is pivotal for implementing effective conservation strategies. Here, we surveyed phyllostomid bats using mist nets in riparian and unflooded forests, flooded savannahs, and conventional rice fields to investigate how changes in habitat quality affect multifaceted diversity from two Colombian farming systems in the Orinoco Llanos: traditional farmlands with high‐intensity agriculture (mainly rice production) and Civil Society Nature Reserves with greater ecosystem protection. We used a unified framework based on Hill numbers for quantifying bat taxonomic, functional, and phylogenetic diversity and modeled the relationship of these diversity facets with landscape variables (habitat cover and patch density) across three spatial scales (0.5, 1.5, 3 km) using Bayesian generalized linear mixed‐effect models. Our results indicate that increasing human activity toward rice monocultures representative of traditional farmlands negatively affected all diversity facets. In contrast, forested habitats associated mainly with riparian forests within private reserves contained higher taxonomic, functional, and phylogenetic diversity than savannahs and rice fields. However, the differences between riparian forests and rice crops were significant only for phylogenetic diversity, indicating loss of evolutionary history after habitat conversion. At the landscape scale, forest cover was a significant predictor for functional (0.5‐ and 3‐km scale) and phylogenetic diversity (0.5 km), and bats responded negatively at the 3‐km scale to rice patch density from a functional diversity perspective. Increasing habitat quality through preserving forest cover and patches should minimize the harmful effects of habitat conversion on multidimensional bat biodiversity. Furthermore, the conservation of riparian forests and the creation of more wildlife‐friendly farming, as practiced in the reserves, should be prioritized to ensure high levels of bat taxonomic, functional, and phylogenetic diversity across Orinoco countryside landscapes.