Anaerobic digestion (AnD) is a process that allows the conversion of organic waste into a source of energy such as biogas, introducing sustainability and circular economy in waste treatment. AnD is an intricate process because of multiple parameters involved, and its complexity increases when the wastes are from different types of generators. In this case, a key point to achieve good performance is optimisation methods. Currently, many tools have been developed to optimise a single AnD plant. However, the study of a network of AnD plants and multiple waste generators, all in different locations, remains unexplored. This novel approach requires the use of optimisation methodologies with the capacity to deal with a highly complex combinatorial problem. This paper proposes and compares the use of three evolutionary algorithms: ant colony optimisation (ACO), genetic algorithm (GA) and particle swarm optimisation (PSO), which are especially suited for this type of application. The algorithms successfully solve the problem, using an objective function that includes terms related to quality and logistics. Their application to a real case study in Catalonia (Spain) shows their usefulness (ACO and GA to achieve maximum biogas production and PSO for safer operation conditions) for AnD facilities.