This paper presents the topic of the management of livestock effluents and, therefore, nutrients (particularly N) in the framework of the biogas supply chain. The bio-refinery will be analyzed as a unique system, from the farm to the biomass produced and sent to anaerobic digestion, focusing on the fate/change of the flow of material and nutrients content through the system. Within four categories of farms considered in the article, integrated ones frequently have a breeding consistency from 90 to 320 heads, according to more extensive or intensive settings. These farms must manage from 3.62 to 12.81 m3 day−1 of slurry and from 11.40 to 40.34 kg day−1 of nitrogen (N) as the sum of excreta from all herd categories. By selecting a hypo-protein diet, a reduction of 10% and 24% for total effluent amount and for N excreted, respectively, can be achieved. Nitrogen can be reduced up to 45% if the crude protein content is limited and a further 0.23% if animals of similar ages, weights and (or) production or management are grouped and fed according to specific requirements. Integrated farms can implement farming activity with biogas production, possibly adding agricultural residues to the anaerobically-digested biomass. Average biogas yields for cattle effluents range from 200 to 400 m3 ton−1 VS (volatile solids). Values from 320 to 672 m3 day−1 of biogas can be produced, obtaining average values from 26 to 54.5 kWe (kilowatt-electric). This type of farm can well balance farm-production profit, environmental protection, animal husbandry well-being and energy self-sufficiency.