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Tropical land-use change is a key driver of global declines in biodiversity and a major source of anthropogenic carbon emissions, yet there is a substantial shortfall in the funding available to tackle these issues. We urgently need mechanisms that can simultaneously tackle both biodiversity and carbon losses, with carbon-based payments for ecosystem services (e.g. REDD+) of particular interest. A critical question is whether such payments offer strong carbon–biodiversity co-benefits via the regrowth of forests on abandoned farmlands (carbon enhancements) for amphibians, which are the most threatened vertebrate group and reach the greatest richness of threatened and small-ranged species in the montane tropics (>1000 m a.s.l.). Here, we study changes in amphibian communities across a typical Andean habitat transition from cattle pasture through secondary forests (8–35 years) to primary forest. As secondary forests mature, they recovered the abundance, species richness, species composition and Red-listed (near threatened and threatened) species typically found in primary forest. By contrast, cattle pasture contained much lower richness of Red-listed species and a different species composition compared to forest. We then reveal positive relationships between carbon stocks and amphibian species richness and abundance, Red-listed species richness and abundance and the similarity of communities to primary forests, confirming significant carbon–biodiversity co-benefits. Our results underscore the high conservation value of secondary forests and the strong potential for carbon and biodiversity recovery. Using carbon-based funding initiatives to support the regrowth of forests on marginal agricultural land is therefore likely to conserve threatened biodiversity in the Tropical Andes.