Climate change and biodiversity loss can be addressed simultaneously by well-planned conservation policies, but this requires information on the alignment of co-benefits under different management actions. One option is to allow forests to naturally regenerate on marginal agricultural land: a key question is whether this approach will deliver environmental co-benefits in an economically viable manner. Here we report on a survey of carbon stocks, biodiversity and economic values from one of the world’s most endemic-rich and threatened ecosystems: the western Andes of Colombia. We show that naturally regenerating secondary forests accumulate significant carbon stocks within 30 years, and support biodiverse communities including many species at risk of extinction. Cattle farming, the principal land use in the region, provides minimal economic returns to local communities, making forest regeneration a viable option despite weak global carbon markets. Efforts to promote natural forest regeneration in the tropical Andes could therefore provide globally significant carbon and biodiversity co-benefits at minimal cost.