Earth’s biodiversity continues to change rapidly through the Anthropocene1, including widespread reordering of species in space2,3 and time4,5. A common expectation of this reordering is that the species composition of sites is becoming increasingly similar across space, known as biotic homogenization, due to anthropogenic pressures and invasive species6,7. While many have argued that homogenisationis a common phenomenon (e.g., 6–10), it is equally plausible that communities can become more different through time, known as differentiation, including through human impacts11,12. Here, we used a novel adaptation of Whittaker’s (1960)13 spatial-scale explicit diversity partition to assess the prevalence of biotic homogenisation and differentiation, and associated changes in species richness at smaller and larger spatial scales. We applied this approach to a compilation of species assemblages from 205 metacommunities that were surveyed for 10-64 years, and 54 ‘checklists’ that spanned 50-500+ years. Scale-dependent changes of species richness were highly heterogeneous, with approximately equal evidence for homogenisation(i.e., lower β-diversity) and differentiation (i.e., higher β-diversity) through time across all regions, taxa and data types. Homogenisation was most often due to increased numbers of widespread species, which tended to increase both local and regional richness through time. These results emphasise that an explicit consideration of spatial scale is needed to fully understand biodiversity change in the Anthropocene.