To achieve climate neutrality in agriculture, whole system changes are needed. This involves the end of the linear resource-product-waste approach, essentially based on increasing production efficiency. Today, the circular approach prevails to optimise resource use efficiency throughout the agri-food system, integrating a recycling phase allowing waste to become a resource, while reducing environmental impacts. Livestock contribute to sustainable agri-food systems by valorising biomass and co-products not directly consumable by humans and transforming them into healthy food. Animal production also contribute to a more efficient agriculture via the diversification of cropping systems and the production of organic fertilizers, while promoting soil fertilization, generating co-products and energy, and providing service diversity. The (re)-integration of crop and livestock farming systems offers likewise the possibility to reduce pollutant emissions, be more efficient at using natural resources, limit the use of external inputs, maintain soil health benefits. However, in a circular system where plants, livestock and management for nutrients and water play central roles, significant challenges can be encountered. We propose to illustrate the linkage between resource, dairy ruminants, manure and soil management such as: very low N and C input systems especially those based on grass and pasture valorisation; the consequences of manure management practices from the animal to the soil on NH3 and GHG emissions and the risk of reverse effects; the substitution of synthetic fertilizers by organic manure, entailing large amounts of manure storage, which may further increase GHG emissions and pollution. Particular attention will be directed to the circularity of diet changes related to sustainable livestock management, crop and soil management choices for animal diets, and at last subsequent manure change, their appropriate use and storage. These illustrations will help to evaluate the reintegration of livestock and cropping systems in a holistic systems-based approach, aiming to mitigate GHGs whilst reducing environmental footprints.