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The lack of safely managed sanitation services is a major global public health and ecological sustainability challenge. Ecological sanitation (EcoSan) technologies designed to close the “poop loop” through the capture, treatment, and beneficial reuse of human feces can meet this interconnected challenge. EcoSan has the potential to mitigate climate change through the reduction of greenhouse gas (GHG) emissions, yet the climate impacts of EcoSan are poorly understood. We measured GHG emissions (carbon dioxide, CO2; methane, CH4; and nitrous oxide, N2O) from two EcoSan operations in Haiti, as well as two anaerobic waste stabilization ponds and a grass field where sewage is known to be illegally deposited. Carbon dioxide was the major constituent of total GHG emissions from both EcoSan systems. Nitrous oxide emissions were similar across both EcoSan systems, however CH4 emissions were significantly higher in the system with moister pile conditions. Highest CH4 fluxes were observed during the first two months of composting in both EcoSan systems. In a paired-comparison, we found that piles with a soil lining had four-fold lower CH4 emissions and three-fold lower N2O emissions compared to piles with a cement lining. Overall climate-forcing effects of emissions from EcoSan were favorable relative to waste stabilization ponds and unmanaged disposal on grass fields. In contrast to EcoSan, CH4 emissions dominated net emissions from waste stabilization ponds, accounting for 94% of net emissions, and N2O emissions were negligible. Methane emissions from waste stabilization ponds were up to 250 times higher than those from EcoSan compost piles. The grass field had a significantly higher CH4 flux than EcoSan, and the highest N2O flux rate observed. Our data suggest that EcoSan systems can contribute to climate change mitigation by reducing GHG emissions relative to alternative sanitation pathways, and EcoSan management conditions can be optimized to minimize emissions.