Earth’s largest tropical peatland, first mapped in 2017, is located within an immense wetland in the Congo Basin, the Cuvette Centrale, covering 167 600 km2. Here, for the first time, we estimate spatio-temporal tree cover loss patterns and the resultant carbon emissions in these forested peatlands using Global Forest Change data from 2001–2021. We find tree cover loss affected 1.4% of the peatlands over 20 years (0.07% yr−1), with 89% occurring in the Democratic Republic of the Congo (DRC, 0.06% yr−1) and 11% in the Republic of the Congo (RoC, 0.008% yr−1). Though low, tree cover loss rates in the peatlands have increased 5x in the DRC and 2x in the RoC between the 2000’s and 2010’s, but are a fraction of the contemporary rate of peatland deforestation in Insular Southeast Asia and are 5x–7x lower than total tree cover loss rates in each country, respectively. The increase in the rate of tree cover loss and in the size of patches of tree cover loss over time and the occurrence of losses near access routes (settlements, roads and waterways) suggests increasing anthropogenic causes. Smaller loss patches are likely due to anthropogenic and natural causes. In the DRC, only 19% of patches were >0.1 km2 in the 2000’s; this rose to 81% in the 2010’s. We detected one anomalously large patch of deforestation (75 km2). A ground-truthed analysis of this patch shows that rice cultivation is driving deforestation on seasonally-flooded forest not underlain by peat and areas of peatland forest underlain by shallow peat. This is a previously unidentified threat to peatland degradation in the Cuvette Centrale. Deforested tropical peatlands can result in significant carbon emissions. We estimate that committed emissions are 108 (76.34–131.81) Tg CO2 from peat decomposition and aboveground biomass loss in the DRC between 2001–2021. Overall, tree cover loss, deforestation and carbon emissions are low compared to other regions with large areas of tropical peatlands, with 98.6% of the Cuvette Centrale peatlands being intact when considering tree cover loss. Ground-based studies including participation from residents of peatland-adjacent communities are acutely needed to validate our findings, improve peatland maps and prioritise local people in future management decisions, and prevent future greater losses.

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