The necessity to investigate suitable alternatives to conventional fossil fuels has increased interest in several renewable energy resources, especially in biomasses that are widely available and make it possible to reach environmental and socio-economic improvements. Among solutions for bioenergy production, anaerobic digestion technology allows biogas production by reusing agricultural residues and agro-industrial by-products. By considering the basic concepts of the Biogasdoneright® method, the objective of this study was to estimate the theoretical potential net electricity and heat production from anaerobic digestion of citrus pulp and olive pomace highly available worldwide. A model was developed and applied in a study area of the Mediterranean basin, where the biogas sector is still very limited despite the importance of both agricultural and agro-industrial activities, especially with regard to citrus and olive cultivation processing. Firstly, the application of a geographical information system (GIS) software tool allowed the estimation of the biogas potentially produced from citrus pulp and olive pomace re-use. Then, the development of a technical assessment demonstrated that 15.9 GWh electricity and 88,000 GJ heat per year could be generated from these by-products, satisfying approximate 17% of the electricity demand of the agricultural sector of the study area (90.2 GWh y⁻¹). The achieved results could be relevant with regard to the intervention priorities established by the European Union related to the planning activities supported by the European Structural and Investment Funds within the Smart Specialisation Strategy.