Assessing how much management of agricultural landscapes, in addition to protected areas, can offset biodiversity erosion in the tropics is a central issue for conservation that still requires cross‐taxonomic and landscape‐scale studies. We measured the effects of Amazonia deforestation and subsequent land‐use intensification in 6 agricultural areas (landscape scale), where we sampled plants and 4 animal groups (birds, earthworms, fruit flies, and moths). We assessed land‐use intensification with a synthetic index based on landscape metrics (total area and relative percentages of land uses, edge density, mean patch density and diversity, and fractal structures at 5 dates from 1990 to 2007). Species richness decreased consistently as agricultural intensification increased despite slight differences in the responses of sampled groups. Globally, in moderately deforested landscapes species richness was relatively stable, and there was a clear threshold in biodiversity loss midway along the intensification gradient, mainly linked to a drop in forest cover and quality. Our results suggest anthropogenic landscapes with high‐quality forest covering >40 % of the surface area may prevent biodiversity loss in Amazonia.