New estimates of greenhouse gas (GHG) emissions from the food system were developed at the country level, for the period 1990–2018, integrating data from crop and livestock production, on-farm energy use, land use and land use change, domestic food transport and food waste disposal. With these new country-level components in place, and by adding global and regional estimates of energy use in food supply chains, we estimate that total GHG emissions from the food system were about 16 CO₂eq yr⁻¹ in 2018, or one-third of the global anthropogenic total. Three quarters of these emissions, 13 Gt CO₂eq yr⁻¹, were generated either within the farm gate or in pre- and post-production activities, such as manufacturing, transport, processing, and waste disposal. The remainder was generated through land use change at the conversion boundaries of natural ecosystems to agricultural land. Results further indicate that pre- and post-production emissions were proportionally more important in developed than in developing countries, and that during 1990–2018, land use change emissions decreased while pre- and post-production emissions increased. We also report results on a per capita basis, showing world total food systems per capita emissions decreasing during 1990–2018 from 2.9 to 2.2 t CO₂eq cap⁻¹, with per capita emissions in developed countries about twice those in developing countries in 2018. Our findings also highlight that conventional IPCC categories, used by countries to report emissions in the National GHG inventory, systematically underestimate the contribution of the food system to total anthropogenic emissions. We provide a comparative mapping of food system categories and activities in order to better quantify food-related emissions in national reporting and identify mitigation opportunities across the entire food system.