Anaerobic bio-digestion/energy generation (ABD/EG) complexes that use animal waste have become increasingly important as renewable energy sources and logistics considerations are essential as animal biomass is of costly transportation due to its high weight per unit of energy generated. To ensure overall economic viability it is necessary to take into account the supply chain network when designing such a complex for at least two main reasons. First, these complexes provide power from energy sources which otherwise would go to waste and a well-designed supply chain network will significantly lower long-term operating costs. Second, because they provide an outlet for farm manure (their feedstock), these complexes allow farmers to expand production capacity whenever environmentally sound animal waste disposal is an active constraint to operations. This paper presents a methodology to design a supply chain which maximizes contribution and minimizes gas loss in the commonly found configuration in which feedstock providers are numerous small farms without on-site bio-digestion units, i.e., a configuration in which in-natura biomass is transported from those small farms to supply a nearby ABD/EG complex serving the region. The paper details three layers of analysis for designing optimal animal waste supply for anaerobic bio-digestion, including model formulation and mathematical solution for each stage. The broadest layer in the methodology is the identification of the optimal ABD/EG complex positioning given farm locations and consequent biomass transportation costs. The middle layer is the specification of the optimal logistics and transportation system, including the prioritization of supplying farms. The operational layer includes scheduling optimal biomass collection from each farm to minimize biogas loss. (C) 2015 Elsevier Ltd. All rights reserved.