Agricultural activities are important contributors to greenhouse gas (GHG) emissions in southern Chile. Three types of agricultural systems coexist within this region: traditional, conventional and agroecological. Historical changes in agricultural practices were identified from bibliographic sources and field surveys of 10 farms of each system type. A similarity analysis between systems was carried out using the survey data, which were also input to the Cool Farm Tool software to estimate GHG emissions of carbon dioxide, methane and nitrous oxide. The main historical changes identified were: (i) replacement of organic inputs by chemical products, (ii) replacement of workforce by agricultural machinery, (iii) decrease in crop diversity and (iv) decrease in total agricultural area. A multivariate analysis showed that agroecological systems are different from the traditional and conventional systems mainly because of the land use and the amount of organic fertiliser applied. However, no significant differences were found in the GHG emissions, which on average were 2999 ± 1521, 3443 ± 2376 and 3746 ± 1837 kg CO₂-eq ha⁻¹ year⁻¹ (traditional, conventional and agroecological, respectively). Enteric fermentation was the main source of emissions in all agricultural systems, therefore methane was the most important GHG. Identifying the sources and practices that produce more emissions should help to improve management to reduce GHG emissions.