Carbon markets are often seen as one of the most economically viable means of supporting biodiversity conservation. By enabling financial investment in nature-based carbon projects, which implement interventions that store and accumulate carbon within natural ecosystems, carbon markets can help to expand conservation action across most of the world. However, fundamental misalignments and shortcomings of carbon markets limit their scalability and effectiveness as a tool for biodiversity conservation. In this Perspective, we examine key technical, social and ecological concerns regarding the use of carbon markets for biodiversity conservation. Requirements for additionality, leakage and permanence, although crucial for accurate carbon credit issuance, do not align with broader ecological requirements for biodiversity conservation. Further, commodification of nature through the generation of nature-based carbon credits can create perverse incentives and negative social and ecological impacts that limit the utility of carbon markets for meaningful environmental stewardship. Although emerging approaches to nature-based carbon projects address these concerns to an extent, optimism around these projects’ utility for supporting conservation should be tempered by an understanding of their limitations. Achieving durable biodiversity outcomes will require integrating carbon markets within wider regulatory, community-based and blended-finance frameworks that safeguard ecological integrity, equity and long-term protection beyond the scope of market instruments. Nature-based carbon projects are widely promoted as delivering both climate and biodiversity benefits. However, carbon accounting requirements can diverge from the needs of biodiversity conservation. This Perspective examines challenges related to additionality, leakage, permanence and unintended social and ecological impacts, highlighting limits to the utility of carbon markets for conservation. Griscom, B. W. et al. Natural climate solutions. Proc. Natl Acad. Sci. USA 114, 11645–11650 (2017). Seddon, N. et al. Understanding the value and limits of nature-based solutions to climate change and other global challenges. Philos. Trans. R. Soc. L... [21775 chars]