With the rapidly expanding ecological footprint of agriculture, the design of farmed landscapes will play an increasingly important role for both carbon storage and biodiversity protection. Carbon and biodiversity can be enhanced by integrating natural habitats into agricultural lands, but a key question is whether benefits are maximized by including many small features throughout the landscape (‘land-sharing’ agriculture) or a few large contiguous blocks alongside intensive farmland (‘land-sparing’ agriculture). In this study, we are the first to integrate carbon storage alongside multi-taxa biodiversity assessments to compare land-sparing and land-sharing frameworks. We do so by sampling carbon stocks and biodiversity (birds and dung beetles) in landscapes containing agriculture and forest within the Colombian Chocó-Andes, a zone of high global conservation priority. We show that woodland fragments embedded within a matrix of cattle pasture hold less carbon per unit area than contiguous primary or advanced secondary forests (>15 years). Farmland sites also support less diverse bird and dung beetle communities than contiguous forests, even when farmland retains high levels of woodland habitat cover. Landscape simulations based on these data suggest that land-sparing strategies would be more beneficial for both carbon storage and biodiversity than land-sharing strategies across a range of production levels. Biodiversity benefits of land-sparing are predicted to be similar whether spared lands protect primary or advanced secondary forests, owing to the close similarity of bird and dung beetle communities between the two forest classes. Land-sparing schemes that encourage the protection and regeneration of natural forest blocks thus provide a synergy between carbon and biodiversity conservation, and represent a promising strategy for reducing the negative impacts of agriculture on tropical ecosystems. However, further studies examining a wider range of ecosystem services will be necessary to fully understand the links between land-allocation strategies and long-term ecosystem service provision.