Human impacts on nature span vast spatial scales that transcend abiotic gradients and biogeographic barriers, yet estimates of biodiversity loss from land-use change overwhelmingly derive from local-scale studies. Using a field dataset of 971 bird species sampled in forest and cattle pasture across 13 biogeographic regions of Colombia, we quantify biodiversity losses from local to near-national scales. Losses are on average 60% worse at the pan-Colombian scale than in individual regions, with underestimation remaining until six to seven biogeographic regions are sampled. Regional losses greatly exceed local losses when beta-diversity is high due to reduced species turnover in pasture across geographic space and elevation. Extrapolation from local-scale studies causes major underestimation of biodiversity loss, emphasizing the need to incorporate spatial structure into measures of change.