This paper presents a novel methodology for planning and operating biogas energy systems based on the transactive energy concept to determine multilevel operating regimes for distributed generation. The developed model is used to manage the production, storage, and dispatch of biogas energy systems to meet the load demands of the biogas producer and support the operation of the distribution network operator. An Integer Linear Programming (ILP) is fitted to optimize the biogas production of the biogas producer, including the operation of the biogas storage systems and their interaction with the network operator. The model’s objective is to maximize benefits for the participating agents in a transactive energy context. The model’s effectiveness is validated using seven case studies involving biogas systems having different operating ranges and modes to achieve enhanced flexibility and reliability for the system operation with a large proportion of intermittent energy resources. The simulation results showed that the approach could effectively manage the operation of biogas systems and their interaction with the network operator. The developed model is suitable for systems fostering net metering charging and real-time pricing.