Abstract Energy conversion strategies based on lignocellulosic and industrial waste streams is considered a challenge in many countries producing huge quantities of biomass. The production of biogas as an energy vector has been gaining attention in the industry sector due to the energy policies for wastes managements or the feasibility of using the biogas for electricity and steam generation. An interesting feedstock alternative for the biogas production is milk whey, one of the main residues of the dairy industry. Additionally the potato stem generated in the harvest stage can be an attractive raw material for biogas production. Co-digestion is the combination of biodegradable raw materials to improve the balance of nutrients in anaerobic digestion. In this context, the characteristics of milk whey and potato stem are not enough to consider it as a good single substrate. However, the synergetic use of these two residues can represent an improvement in biogas production. The biogas production was calculated in Aspen Plus software using stoichiometric and kinetic models based on the experimental characterization of both materials. Through seven different scenarios: potato stem digestion, milk whey digestion and five co-digestion relations of both materials. Heat and electricity generation using biogas was analyzed. Then the generation of heat and electricity was simulated, where the economic profit was evaluated in terms of the production cost, capital cost, revenues and net present value. In terms of biogas production, the scenarios that involved high organic load were the best. For the economic assessment the raw material cost had the most influence over the total processing cost (80% approximately). However, even if energy is produced it is necessary to include the valorization of the digestate as biofertilizer in order that the different scenarios present economic viability.