With intensifying demands for food and biofuels, a critical threat to biodiversity is agricultural expansion into native tropical ecosystems. Tropical agriculture, particularly intensive agriculture, often supports few native organisms, and consequently has been largely overlooked in conservation planning; yet, recent work in the Neotropics demonstrates that tropical agriculture with certain features can support significant biodiversity, decades after conversion to farmland. It remains unknown whether this conservation value can be sustained for centuries to millennia. Here, we quantify the bird diversity affiliated with agricultural systems in southwest India, a region continuously cultivated for >2,000 years. We show that arecanut palm (Areca catechu) production systems retain 90% of the bird species associated with regional native forest. Two factors promote this high conservation value. First, the system involves intercropping with multiple, usually woody, understory species and, thus, has high vertical structural complexity that is positively correlated with bird species richness. Second, the system encompasses nearby forests, where large quantities of leaf litter are extracted for mulch. The preservation of these forests on productive land traces back to their value in supplying inputs to arecanut cultivation. The long-term biodiversity value of an agricultural ecosystem has not been documented in South and Southeast Asia. Our findings open a new conservation opportunity for this imperiled region that may well extend to other crops. Some of these working lands may be able to sustain native species over long-time scales, indicating that conservation investments in agriculture today could pay off for people and for nature.