Agriculture is widely recognized as a source of considerable greenhouse gas (GHG) emissions, with opportunities for mitigation. The limited capacity to identify and collect reliable activity data and to quantify emissions by sources and removals by sinks needs to be addressed. One proposed solution is to adapt IPCC methodologies that include estimations of both CO2 emissions and carbon sequestration in agricultural systems, which were applied to Colombia at the farm level in this study. The aim of this work was to provide an assessment of GHG balances through these IPCC methodologies to identify potential GHG mitigation in sustainable agricultural systems used in Colombia that provide acceptable GHG trade‐offs to the atmosphere. Agroforestry systems made the largest contribution to this mitigation potential because of the potential to sequester carbon in both soil and biomass, giving a negative GHG emission to the atmosphere. GHG balance analysis at the Colombian farm level indicated that conventional agriculture with pastures of Pennisetum clandestinum in rotation with potatoes (PRP) in the Andean zone of Nariño (Colombia) is a large emitter of GHG with 9.1 ton CO2eq ha−1 year−1. On the other hand, in livestock systems in the Andean zone (Antioquia), intensive silvopastoral systems with 500 Eucalyptus tereticornis trees ha−1 (SSPi) on pastures is a great neutralizer of GHG emissions, accounting for −26.6 t CO2eq ha−1 year−1. Agroforestry systems play a leading role, as crop rotation and improved pastures can represent a GHG mitigation opportunity for sustainable agricultural production at the farm level in Colombia. © 2021 Society of Chemical Industry and John Wiley & Sons, Ltd.