Thermophilic composting within ecological-based sanitation systems (EcoSan) facilitates a biogeochemical transformation of pathogenic solid materials into a sanitary organic soil amendment. Recent work suggests that, in addition to recycling nutrients and eliminating pathogens, thermophilic composting during EcoSan can lower greenhouse gas emission compared to other waste treatment practices, however empirical observations of gas fluxes are few. Data are particularly lacking from urban areas in the global south where innovation in sanitary infrastructure is a sustainable development priority. We quantified greenhouse gas emissions with intensive chamber-based flux sampling over three cycles of thermophilic composting at an established EcoSan operation serving an urban community in northern Haiti. We asked: (1) How do dynamics of greenhouse gases vary throughout the lifetime of the compost pile and the different operational stages? (2) What fraction of initial carbon and nitrogen content is lost via gas fluxes and how does this compare to internationally defined emissions factors? (3) How can different pile management options further mitigate emissions? We found methane emissions were highest in the thermophilic stage, ranging from 5-20 µmol m-2 s-1, and dominated the global warming potential of the entire operation. Approximately 0.1-0.5% of initial pile carbon was emitted as methane while only 0.05-0.3% of initial pile nitrogen was emitted as nitrous oxide, both at the low end of IPCC emissions factor ranges for manure composting. In paired-pile experiments, we found that improved pile drainage could further mitigate methane emissions, as could use of a thinner layer of cover material. This study provides some of the first detailed observations of greenhouse gas dynamics during the thermophilic composting of human waste and our results suggest that climate mitigation potential associated with composting-based EcoSan is greater than previously thought.