Tropical peatlands store around one-sixth of the global peatland carbon pool (105 gigatonnes), equivalent to 30% of the carbon held in rainforest vegetation. Deforestation, drainage, fire and conversion to agricultural land threaten these ecosystems and their role in carbon sequestration. In this Review, we discuss the biogeochemistry of tropical peatlands and the impacts of ongoing anthropogenic modifications. Extensive peatlands are found in Southeast Asia, the Congo Basin and Amazonia, but their total global area remains unknown owing to inadequate data. Anthropogenic transformations result in high carbon loss and reduced carbon storage, increased greenhouse gas emissions, loss of hydrological integrity and peat subsidence accompanied by an enhanced risk of flooding. Moreover, the resulting nutrient storage and cycling changes necessitate fertilizer inputs to sustain crop production, further disturbing the ecosystem and increasing greenhouse gas emissions. Under a warming climate, these impacts are likely to intensify, with both disturbed and intact peat swamps at risk of losing 20% of current carbon stocks by 2100. Improved measurement and observation of carbon pools and fluxes, along with process-based biogeochemical knowledge, is needed to support management strategies, protect tropical peatland carbon stocks and mitigate greenhouse gas emissions. Tropical peatlands hold around 105 gigatonnes of carbon but are increasingly affected by anthropogenic activities. This Review describes the biogeochemistry of these systems and how deforestation, fire, drainage and agriculture are disturbing them. Tropical peatlands are important in terms of the global carbon cycle and in efforts to combat climate change, with a growing recognition of their potential role in natural climate solutions.Tropical peatlands occupy approximately 440,000 km2 across Southeast Asia, Central Africa and South and Central America, and are mostly forested. They are among the world’s most carbon-dense ecosystems with a belowground carbon stock of about 105 gigatonnes (Gt).Although tropical peatlands in Africa and in South and Central America remain largely intact, those in Southeast Asia have undergone widespread transformations owing to deforestation, drainage and agricultural conversion.Land-use changes result in rapid peat carbon loss, high greenhouse gas emissions, land subsidence, changes in hydrology and nutrient cycling, and an increased risk of fire.Management priorities include protection of the carbon sink function of intact forested peatlands; restoration of degraded, forested peatlands; and improved management of agricultural peatlands by raising water levels to mitigate carbon losses and greenhouse gas emissions.The response of tropical peatlands and their carbon stocks to anthropogenic warming and associated changes in hydroclimate remain an area of uncertainty. Tropical peatlands are important in terms of the global carbon cycle and in efforts to combat climate change, with a growing recognition of their potential role in natural climate solutions. Tropical peatlands occupy approximately 440,000 km2 across Southeast Asia, Central Africa and South and Central America, and are mostly forested. They are among the world’s most carbon-dense ecosystems with a belowground carbon stock of about 105 gigatonnes (Gt). Although tropical peatlands in Africa and in South and Central America remain largely intact, those in Southeast Asia have undergone widespread transformations owing to deforestation, drainage and agricultural conversion. Land-use changes result in rapid peat carbon loss, high greenhouse gas emissions, land subsidence, changes in hydrology and nutrient cycling, and an increased risk of fire. Management priorities include protection of the carbon sink function of intact forested peatlands; restoration of degraded, forested peatlands; and improved management of agricultural peatlands by raising water levels to mitigate carbon losses and greenhouse gas emissions. The response of tropical peatlands and their carbon stocks to anthropogenic warming and associated changes in hydroclimate remain an area of uncertainty.