The state of Jalisco is the largest livestock producer in Mexico, leading in the production of swine, eggs, and milk. This immense production generates enormous amounts of waste as a byproduct of the process itself. The poor management of livestock-derived waste can lead to multiple environmental problems like nutrient accumulation in soil, water eutrophication, and air pollution. The aim of this work is to establish a replicable geographic information system (GIS)-based methodology for selecting priority sites in which to implement anaerobic digestion units. These units will use multiple parameters that evaluate environmental risks and viability factors for the units themselves. A weighted overlay analysis was used to identify critical regions and, based on the results, clusters of individual livestock production units (LPUs) across the state were selected. Nitrogen and phosphorus recovery, as well as the energetic potential of the selected clusters, were calculated. Four clusters located mainly in the Los Altos region of Jalisco were selected as critical and analyzed. The results indicate that Jalisco has the potential to generate 5.5% of its total electricity demand if the entirety of its livestock waste is treated and utilized in centralized anaerobic digestion units. Additionally, 49.2 and 31.2 Gg of nitrogen and phosphorus respectively could be valorized, and there would be an estimated total reduction of 3012.6 Gg of carbon dioxide equivalent (CO2eq).