Interest in economically and ecologically sustainable cocoa has grown in recent years. Cocoa-based agroforestry systems are promoted as a potential win-win option for long-term yields, multiple benefits, and the preservation of biodiversity. Yet, even though recent studies have shown such agroforests can support biodiversity, their value relative to natural areas and open-land systems is not fully known. We estimated the biodiversity intactness (BII) of different land uses associated with cocoa-driven land-use change using mixed-effects models. We distinguished between agroforests established under natural shade and those grown from open land, and compared these to intensively grown cropland (including cocoa monoculture), and primary and secondary forest. We found that species richness in cocoa-based agroforestry systems, under both natural and planted shade, was lower than in primary forests but higher than in open-land systems. However, we found that land-use history influenced the biodiversity intactness of agroforests: whilst open-land-derived cocoa-based agroforestry systems and forest-derived cocoa-based agroforestry systems share similar species richness, open-land-derived cocoa-based agroforestry systems have lower community similarity to primary forest than forest-derived cocoa-based agroforestry systems. The results highlight that high levels of BII can be sustained by retaining the natural shade in existing agroforestry systems, but also that incentivising planted shade agroforestry can enhance biodiversity intactness in degraded areas whilst delivering co-benefits. Importantly, the results highlight that cocoa planning seeking to achieve biodiversity benefits should consider the direction of land use and biodiversity transitions.