A small subset of protected areas are a highly significant source of carbon emissions.

Protected areas (PAs) aim to protect multiple ecosystem services. However, not all are well protected. For the first time, using published carbon and forest loss maps, we estimate carbon emissions in large forest PAs in tropical countries (N = 2018). We found 36 ± 16 Pg C stored in PA trees, representing 14.5% of all tropical forest biomass carbon. However the PAs lost forest at a mean rate of 0.18% yr from 2000-2012. Lower protection status areas experienced higher forest losses (e.g. 0.39% yr in IUCN cat III), yet even highest status areas lost 0.13% yr (IUCN Cat I). Emissions were not evenly distributed: 80% of emissions derived from 8.3% of PAs (112 ± 49.5 Tg CO yr; n = 171). Unsurprisingly the largest emissions derived from PAs that started with the greatest total forest area; accounting for starting forest area and relating that to carbon lost using a linear model (r = 0.41), we found 1.1% outlying PAs (residuals >2σ; N = 23), representing 1.3% of the total PA forest area, yet causing 27.3% of all PA emissions. These results suggest PAs have been a successful means of protecting biomass carbon, yet a subset causing a disproportionately high share of emissions should be an urgent priority for management interventions.