Biogas is a fuel obtained from organic waste fermentation and can be an interesting solution for producing electric energy, heat and fuel. Recently, many European countries have incentivized the production of biomethane to be injected into natural gas grids or compressed and used as biofuel in vehicles. The introduction of an upgrading unit into an existing anaerobic digestion plant to convert biogas to biomethane may have a strong impact on the overall energy balance of the systems. The amount of biomethane produced may be optimized from several points of view (i.e., energy, environmental and economic). In this paper, the mass and energy fluxes of an anaerobic digestion plant were analyzed as a function of the biogas percentage sent to the upgrading system and the amount of biomethane produced. A numerical model of an anaerobic digestion plant was developed by considering an existing case study. The mass and energy balance of the digesters, cogeneration unit, upgrading system and auxiliary boiler were estimated when the amount of produced biomethane was varied. An internal combustion engine was adopted as the cogeneration unit and a CO₂ absorption system was assumed for biogas upgrading. Results demonstrated that the energy balance of the plant is strictly dependent on the biomethane production and that an excess of biomethane production makes the plant totally dependent on external energy sources. As for the environmental impact, an optimal level of biomethane production exists that minimizes the emissions of equivalent CO₂. However, high biomethane subsides can encourage plant managers to increase biomethane production and thus reduce CO₂ savings.