Greenhouse gases (GHG) levels in the atmosphere has been significantly increased, in the last few years, thereby contributing to the damaging effects caused by the global warming. Particularly, the average temperature on Earth in the past decade increased by 1.09 °C compared to the reference data from 1850 to 1900, according to the recent Intergovernmental Panel on Climate Change (IPCC) report. In this context, it is widely accepted that a considerable amount of the anthropogenic GHG emissions stems from highly intensified agricultural and livestock practices. This kind of models try to maximize their productive rates at any cost, using fewer natural resources and extremely-high stocking rates, therefore diminishing environmental sustainability and animal welfare. In 2014 the EU Commission stated that every EU member should reduce their GHG emissions by 30% by 2030 compared to the 2005 level, promoting in consequence the progressive disappearance of super intensive productive models in the primary sector. In addition, there is in the present society an increasing trend towards more sustainable productive and management activities, such as those promoted by extensive and/or organic systems. All this seems to point to a slow yet unstoppable transition towards more sustainable production systems, such as organic systems. In organic livestock systems, the main sources of GHG emissions are associated with enteric fermentation in ruminants’ farms or with manure management for pig farms, but not with purchasing feed inputs or using chemical products. Several studies have shown that, a priori, extensive systems, standing out organic practices, have a lower environmental impact than intensive systems because they use their own inputs instead of external ones, thereby reducing their energy consumption and, consequently, the fossil fuels they require. Moreover, they could also generate added value from an economic and environmental point of view. Therefore, it could be assumed that organic farming will be crucial in the future food systems. According to the International Federation of Organic Agriculture Movements (IFOAM), in a foreseeable scenario where organic farming accounts for 50% of food production, it would yield a potential reduction of 12–14% in the GHG emissions from farming industry in the EU. Measuring the carbon footprint of livestock farming of extensive systems and specifically, of organic ones, is a major objective to sustain the current productive transition. However, GHG emissions derived from farming systems are considered quite complex and heterogeneous and, in addition, there is a wide variety of methods that can be used to calculate or estimate the carbon footprint. All this together make the measurement and comparison of GHG emissions from different geographical and cultural areas a challenging task. Among those methods, on of the most internationally-recognized is the well-known Life Cycle Assessment (LCA), which allows the measurement of GHG emissions both in conventional and organic productive systems. But also, the emission factors involved in this calculation will determine the carbon footprint obtained, as it is quite different consider that the limits of the system remain on the farm itself or, on the contrary, consider the entire life cycle of the inputs (transport, manufacturing, etc.). The organic livestock farming model might be a feasible strategy for reducing GHGs and, therefore, for meeting the global food demand while maintaining environmental sustainability and animal welfare.