Smallholder agriculture is the main driver of deforestation in the western Amazon, where terrestrial biodiversity reaches its global maximum. Understanding the biodiversity value of the resulting mosaics of cultivations and secondary forest is therefore crucial for conservation planning. However, Amazonian communities are organized across multiple forest‐types that support distinct species assemblages, and little is known about smallholder impacts across the range of forest habitats that are essential for sustaining biodiversity. We address this issue with a large‐scale field inventory of birds and trees in primary forest and smallholder agriculture in northern Peru, spanning three key forest‐types that structure Amazonian biodiversity. For...