Evaluation of the primary forests in the Brazilian state of Pará shows that anthropogenic disturbance can more than double the loss of biodiversity expected from deforestation. The protection of tropical forests is integral to many biodiversity conservation strategies. These strategies have focused on the maintenance of forest cover, but anthropogenic disturbance, in the form of logging, wildfires and landscape disturbance, has the potential to reduce the conservation value of remaining tropical forests. Jos Barlow et al. assess the combined effect of these forms of anthropogenic disturbance on the conservation value of primary forest in the state of Pará in the Brazilian Amazon, using occurrence data on 1,538, 460 and 156 species of plants, birds and dung beetles, respectively, collected along a gradient of forest cover. They find that anthropogenic disturbance has more than doubled the biodiversity loss expected from deforestation alone in catchments comprising 69–80% forest cover. They say that their findings call for policy interventions that go beyond the maintenance of forest cover, if the rich diversity of tropical forest ecosystems is to be safeguarded. Concerted political attention has focused on reducing deforestation1,2,3, and this remains the cornerstone of most biodiversity conservation strategies4,5,6. However, maintaining forest cover may not reduce anthropogenic forest disturbances, which are rarely considered in conservation programmes6. These disturbances occur both within forests, including selective logging and wildfires7,8, and at the landscape level, through edge, area and isolation effects9. Until now, the combined effect of anthropogenic disturbance on the conservation value of remnant primary forests has remained unknown, making it impossible to assess the relative importance of forest disturbance and forest loss. Here we address these knowledge gaps using a large data set of plants, birds and dung beetles (1,538, 460 and 156 species, respectively) sampled in 36 catchments in the Brazilian state of Pará. Catchments retaining more than 69–80% forest cover lost more conservation value from disturbance than from forest loss. For example, a 20% loss of primary forest, the maximum level of deforestation allowed on Amazonian properties under Brazil’s Forest Code5, resulted in a 39–54% loss of conservation value: 96–171% more than expected without considering disturbance effects. We extrapolated the disturbance-mediated loss of conservation value throughout Pará, which covers 25% of the Brazilian Amazon. Although disturbed forests retained considerable conservation value compared with deforested areas, the toll of disturbance outside Pará’s strictly protected areas is equivalent to the loss of 92,000–139,000 km2 of primary forest. Even this lowest estimate is greater than the area deforested across the entire Brazilian Amazon between 2006 and 2015 (ref. 10). Species distribution models showed that both landscape and within-forest disturbances contributed to biodiversity loss, with the greatest negative effects on species of high conservation and functional value. These results demonstrate an urgent need for policy interventions that go beyond the maintenance of forest cover to safeguard the hyper-diversity of tropical forest ecosystems.