The present article exposes a model of Mixed Integer Linear Programming (MILP) as a support for strategic decision making, guided to the location of facilities in ethanol supply chains under a configuration of collection centers of raw material and production plants, directly impacting costs related to logistics and operations. The model is applied to the supply chain for the production of ethanol from two by-products and a coffee residue (pulp, mucilage, and stems, respectively) in Colombia. The results obtained by the model allow identifying locations for the corresponding links to the three types of biomass considered, and the flows of raw material between coffee producing departments and collection centers, from the latter to production plants, and from this, where the transformation of ethanol to mixing centers is generated.