Selective logging is the most widespread driver of tropical forest disturbance. As such, it is critically important to identify at which spatial scale logging intensity should be measured and whether there are clear thresholds in the relationship between logging intensity and its impacts on biodiversity or ecological processes. We address this using a robust before-and–after logging experimental design in the Brazilian Amazon, using a gradient of logging intensity measured at two different spatial scales. We assessed the impacts of selective logging using dung beetle communities and their ecological functions of dung removal and soil bioturbation. Our findings provide novel empirical evidence that biological consequences from Reduced Impact Logging (RIL) depend strongly on the scale at which logging intensity is measured: dung beetle local species richness and composition were strongly associated with logging intensity measured at a 10ha scale, while dung beetle-mediated soil bioturbation was more strongly associated with logging intensity measured across 90ha. Contrary to expectations, we found concave-shaped relationships between logging intensity and biodiversity and ecosystem functioning, demonstrating that sensitive dung beetle species and important processes may be lost following even low intensity anthropogenic forest disturbances. Taken together, these results suggest that production forests in the tropics need to reconsider the scale at which logging intensity is regulated, and put in place measures that further incentivise land sparing to enhance biodiversity conservation.