Microbial fuel cell (MFC) is a promising renewable energy technology wherein electrical power is obtained from the metabolism of microorganisms and simultaneous wastewater treatment. For efficient operation, MFCs need a control system for balance across fuel supply, mass, charge, and electrical load. Control-oriented models help in developing model based control strategies. Control-oriented parametrized model of single chamber single microorganism is presented in this paper. A backstepping and an adaptive backstepping control of a single chamber microbial fuel cell (MFC) with single microorganism kinetics, is presented. The key advantage of the backstepping scheme is its ability to handle systems with different relative degrees (difference between number of poles and zeros). In order to control the substrate concentration, the dilution rate of the MFC is used as a manipulated input variable. An adaptive action is provided for robustness to model uncertainties and online parameter estimation is performed. Lyapunov stability analysis ensures a convergent control scheme, and the control performances are illustrated using MATLAB/Simulink. •Control-Oriented Parametrized model for Microbial Fuel Cell is proposed.•A novel adaptive backstepping control strategy is developed.•Adaptive control strategy applied to single chamber single population MFC.•Using dilution rate as input variable, substrate concentration is controlled.