In this paper we consider the control of the methane flow rate in biogas production using a continuous stirred tank reactor or a fixed bed digester. The goal is to regulate the methane flow rate in order to match an energy demand in spite of variations in the waste concentrations. For this purpose, a two step (acidogenesis-methanogenesis) nonlinear mass balance model is considered. Due to the costs and complexity of the measurements an observer based estimator is designed for the acidogenesis reaction rate. The stability of the observation part is proved and its implementation with the designed control laws for both the methane flow rate and the acetate concentration in the reactor are confirmed by simulations.