The increasing proportion of intermittent renewable energies asks for further technologies for balancing demand and supply in the energy system. In contrast to other countries, Germany is characterized by a high installed capacity of dispatchable biogas plants. For this paper, we analyzed the total system costs varying biogas extension paths and modes of operation for the period of 2016–2035 by using a non-linear optimization model. We took variable costs of existing conventional power plants, as well as variable costs and capital investments in gas turbines, Li-ion batteries, and pumped-storage plants into account. Without the consideration of the costs for biogas plants, an increasing proportion of biogas plants, compared to their phase out, reduces the total system costs. Furthermore, their flexible power generation should be as flexible as possible. The lowest total system costs were calculated in an extension path with the highest rate of construction of new biogas plants. However, the highest marginal utility was assessed by a medium proportion of flexible biogas plants. In conclusion, biogas plants can be a cost-effective option to integrate intermittent renewable energies into the electricity system. The optimal extension path of biogas plants depends on the future installed capacities of conventional and renewable energies.