This study employs life cycle assessment (LCA) for the calculation of the balance (emissions minus sequestration) of greenhouse gas emissions (GHG) in the organic livestock production systems of dehesas in the southwest region of Spain. European organic production standards regulate these systems. As well as calculating the system’s emissions, this method also takes into account the soil carbon sequestration values. In this sense, the study of carbon sequestration in organic systems is of great interest from a legislation viewpoint. The results reveal that the farms producing meat cattle with calves sold at weaning age provide the highest levels of carbon footprint (16.27 kg of carbon dioxide equivalent (CO2eq)/kg of live weight), whereas the farms with the lowest levels of carbon emissions are montanera pig and semi-extensive dairy goat farms, i.e., 4.16 and 2.94 kg CO2eq/kg of live weight and 1.19 CO2eq/kg of fat and protein corrected milk (FPCM), respectively. Enteric fermentation represents 42.8% and 79.9% of the total emissions of ruminants’ farms. However, in pig farms, the highest percentage of the emissions derives from manure management (36.5%–42.9%) and animal feed (31%–37.7%). The soil sequestration level has been seen to range between 419.7 and 576.4 kg CO2eq/ha/year, which represents a considerable compensation of carbon emissions. It should be noted that these systems cannot be compared with other more intensive systems in terms of product units and therefore, the carbon footprint values of dehesa organic systems must always be associated to the territory.