Habitat loss and degradation is the most pervasive threat to tropical biodiversity worldwide. Amazonia sits at the frontline of efforts to both improve the productivity of tropical agriculture and prevent the loss of biodiversity. To date our understanding of the biodiversity impacts of agricultural expansion in Amazonia is restricted to findings from small scale studies that typically assess the importance of a limited number of land-use types. Here we investigate local and landscape-scale responses of Amazonian avian assemblages to land-cover changes across a gradient of land-use intensity ranging from undisturbed primary forest to mechanised agriculture in 36 drainage catchments distributed across two large regions of the eastern Brazilian Amazon. We found that species richness of forest-associated birds declined progressively along this gradient, accompanied by marked shifts in assemblage composition. We found significant changes in species composition, but not richness, between primary forests that had been subject to different levels of disturbance from logging and fire. Secondary forests retained levels of species richness intermediate between primary forests and production areas, but lacked many forest-dependent species. Production areas (arable crops, cattle pastures and plantation forests) all retained far fewer species than any forest habitat, and were largely dominated by taxa commonly associated with open areas. Diversity partitioning revealed that species composition varied the most among undisturbed forest transects, and steadily decreased with increasing forest degradation and land-use intensity. Our results emphasise the importance of protecting both remaining areas of primary forest in private lands, as well as protecting the same forests from further disturbance events.