Cold chains are essential components of agrifood system activities, from storage and food processing to transport, retail, and household consumption. We devise a comprehensive methodology, validated against established data, to estimate both direct (due to refrigerant use) and indirect (from energy use) greenhouse gas emissions from agrifood system cold chains, expanding previous approaches, which had focused on direct emissions only. We found that in 2022, world-total indirect emissions from energy use in cold chains were more than twice the direct component from refrigerants. This resulted in a new estimate of world-total GHG emissions from agrifood system cold chains of 1.32 Gt CO2eq in 2022, with significant growth over the past two decades (0.52 Gt CO2eq in 2000). Household consumption and food processing represented the most significant contributors to agrifood system emissions from cold chains, together representing in 2022 three-fourths of the total. These results align well with known global patterns of energy use in the refrigeration sector and highlight the importance of targeting cold chains within agrifood system with GHG emission mitigation actions.