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Tropical agriculture is a major driver of biodiversity loss, yet it can provide conservation opportunities, especially where protected areas are inadequate. To investigate the long-term biodiversity capacity of agricultural countryside, we quantified bird population trends in Costa Rica by mist netting 57,255 birds of 265 species between 1999 and 2010 in sun coffee plantations, riparian corridors, secondary forests, forest fragments, and primary forest reserves. More bird populations (69) were declining than were stable (39) or increasing (4). Declines were common in resident, insectivorous, and more specialized species. There was no relationship between the species richness of a habitat and its conservation value. High-value forest bird communities were characterized by their distinct species composition and habitat and dietary functional signatures. While 49% of bird species preferred forest to coffee, 39% preferred coffee to forest and 12% used both habitats, indicating that coffee plantations have some conservation value. Coffee plantations, although lacking most of the forest specialists, hosted 185 bird species, had the highest capture rates, and supported increasing numbers of some forest species. Coffee plantations with higher tree cover (7% vs. 13%) had more species with increasing capture rates, twice as many forest specialists, and half as many nonforest species. Costa Rican countryside habitats, especially those with greater tree cover, host many bird species and are critical for connecting bird populations in forest remnants. Diversified agricultural landscapes can enhance the biodiversity capacity of tropical countryside, but, for the long-term persistence of all forest bird species, large (> 1,000 ha) protected areas are essential.