Microbial fuel cells are one of the most important elements in the renewable energy supply chain. To increase the effi ciency and performance of the fuel cell, designing a suitable control method is essential to achieve reliable performance and output stability. By considering the parametric uncertainties on the microbial fuel cell model as well as nonlinear terms, this paper presents a novel fi nite time adaptive sliding mode control method that achieves optimal performance of fuel cell in a fi nite time and also ensures the stability of the closed loop system. Sliding mode method without linearization or elimination of nonlinear terms has been used as a robust method to overcome uncertainty eff ects and guarantees proper operation of the fuel cell in the presence of the eff ects. The fi nite time convergence of the states is also assured by using of the proposed method. Furthermore, it uses an adaptive method to determine the sliding mode control coeffi cients which eliminates the necessity to know the upper bound of uncertainty. Finally, the simulation results show the effi ciency and stability of the proposed method in diff erent operating conditions.