Food waste is a dominant organic constituent of landfills, and a large global source of greenhouse gases. Composting food waste presents a potential opportunity for emissions reduction, but data on whole pile, commercial-scale emissions and the associated biogeochemical drivers are lacking. We used a non-invasive micrometeorological mass balance approach optimized for three-dimensional commercial-scale windrow compost piles to measure methane (CH4), nitrous oxide (N2O), and carbon dioxide (CO2) emissions continuously during food waste composting. Greenhouse gas flux measurements were complemented with continuous oxygen (O2) and temperature sensors and intensive sampling for biogeochemical processes. Emission factors (EF) ranged from 6.6 to 8.8 kg CH4–C/Mg wet food waste and were driven primarily by low redox and watering events. Composting resulted in low N2O emissions (0.01 kg N2O–N/Mg wet food waste). The overall EF value (CH4 + N2O) for food waste composting was 926 kgCO2e/Mg of dry food waste. Composting emissions were 38–84% lower than equivalent landfilling fluxes with a potential net minimum savings of 1.4 MMT CO2e for California by year 2025. Our results suggest that food waste composting can help mitigate emissions. Increased turning during the thermophilic phase and less watering overall could potentially further lower emissions.