To better understand how ecosystems are changing, a multifaceted approach to measuring biodiversity that considers species richness (SR) and evolutionary history across spatial scales is needed. Here, we compiled 162 datasets for fish, bird and plant assemblages across the globe and measured how taxonomic and phylogenetic diversity changed at different spatial scales (within site α diversity and between sites spatial β diversity). Biodiversity change is measured from these datasets in three ways: across land use gradients, from species lists, and through sampling of the same locations across two time periods. We found that local SR and phylogenetic α diversity (Faith's PD (phylogenetic diversity)) increased for all taxonomic groups. However, when measured with a metric that is independent of SR (phylogenetic species variation, PSV), phylogenetic α diversity declined for all taxonomic groups. Land use datasets showed declines in SR, Faith's PD and PSV. For all taxonomic groups and data types, spatial taxonomic and phylogenetic β diversity decreased when measured with Sorensen dissimilarity and phylogenetic Sorensen dissimilarity, respectively, providing strong evidence of global biotic homogenization. The decoupling of α and β diversity, as well as taxonomic and phylogenetic diversity, highlights the need for a broader perspective on contemporary biodiversity changes. Conservation and environmental policy decisions thus need to consider biodiversity beyond local SR to protect biodiversity and ecosystem services.