The conversion of tropical rainforest to agricultural systems such as oil palm alters biodiversity across a large range of interacting taxa and trophic levels. Yet, it remains unclear how direct and cascading effects of land-use change simultaneously drive ecological shifts. Combining data from a multi-taxon research initiative in Sumatra, Indonesia, we show that direct and cascading land-use effects alter biomass and species richness of taxa across trophic levels ranging from microorganisms to birds. Tropical land use resulted in increases in biomass and species richness via bottom-up cascading effects, but reductions via direct effects. When considering direct and cascading effects together, land use was found to reduce biomass and species richness, with increasing magnitude at higher trophic levels. Our analyses disentangle the multifaceted effects of land-use change on tropical ecosystems, revealing that biotic interactions on broad taxonomic scales influence the ecological outcome of anthropogenic perturbations to natural ecosystems.