Biomethane represents one of the solutions towards the European Union (EU) energy transition, being capable to decarbonize the EU’s energy system and to reduce the dependence on imported natural gas, as underlined by the “REPowerEU” energy policy program. As its production is expected to expand primarily from biogenic wastes and residues, such as agricultural residues and animal effluents, it is necessary to make its deployment cost-efficient, taking into account factors such as local resources, existing infrastructure, and raw material and investment costs. From this perspective, this paper proposes a replicable predictive model for locating agro-biomethane plants according to raw material potential, relative economic factors, and territorial characteristics. To this end, an analysis was conducted in the Geographic Information System environment, based on location theory. The analysis included testing the minimum transport cost of feedstock in a case study of a rural area in Southern Italy. Three optimal locations for 2 MW size plants were selected where some key element conditions had been identified. The research findings may provide useful information for the EU policymakers in defining more specific energy planning strategies, in accordance with the REPowerEU objectives, addressing the increase in biomethane production by 2030.