A generalized low-order model of the biofilm in a microbial fuel cell (MFC), suitable for use in real-time engineering applications, is presented. It is based on the description of the charge transfer, diffusion process, and charge accumulation in the biofilm. Since the dynamic processes in an MFC are ruled mainly by the biofilm, it can be used for many different diffusion-based MFC types by just changing the boundary conditions. Different mode operations like batch, fed-batch, continuous, etc., are also possible. The time-responses of voltage, substrate concentration on the surface of the electrode, and Faradaic and capacitive currents have been tested under several experimental conditions.