Global biodiversity conservation significantly depends on bringing conservation measures to the agricultural production systems that dominate the earth's surface. One of the leading candidates for wildlife-friendly farming in the megadiverse lowland tropics is shade-grown cocoa. However, tropical farmers increasingly believe that shade reduces yield and consequently, are removing most shade trees from their farms. Conservation goals therefore conflict with production imperatives. Nevertheless, we tested the trade-off between production and biodiversity conservation in the critical conservation area of the Ecuadorean Chocó and found that both farmers and biodiversity would benefit from an increase in shade. This rare partial win-win situation in wildlife-friendly farming permits the creation of a sustainable, economically sensitive certification and geographic indication for biodiversity-friendly chocolate. We suggest that similar trade-off studies be carried out in other agroforestry regions of conservation importance, not least to establish the probable sustainability of conservation initiatives in production-centered landscapes.