Changes in biodiversity reflect processes acting at multiple spatial scales, including globally, among habitats and within communities. This complexity makes it difficult to analyse the mechanisms that change biodiversity over time. To resolve this, we propose a novel approach to partition temporal changes in biodiversity into contributions from selection at multiple scales. We apply this approach to study changes in the biodiversity of invertebrate herbivores from a large-scale, plant community experiment. Though the experiment was designed to foster distinct insect communities due to differences in host plants, our approach shows that selection among these treatments was a negligible facet of diversity change. Instead, the dominant source of community dynamics was rapid changes in the relative abundances of individual species. These shifts produced surprisingly small changes in biodiversity. More broadly our work highlights how total change in biodiversity across a biogeographic region can be partitioned into logically distinct mechanisms.