In this work an anaerobic digester is controlled using input-output linearization and Lyapunov-like function methods. It is assumed that model parameters are unknown, time-varying, and bounded, and upper or lower bounds are also unknown. To tackle the effect of input saturation, a state observer is designed. The tracking and observer errors are defined in terms of the noisy measured output instead of ideal output, given by the mathematical model. The design of the observer mechanism and the update laws is based on the Lyapunov-like function technique, whereas the design of the control law is based on the input-output linearization method. In this paper two important properties of the controlled system are proven. First, the observer error converges asymptotically to a residual set whose size is user-defined, and such convergence is not disrupted, neither by the input saturation nor by the parameter uncertainties. Second, when the control input is nonsaturated the tracking error converges to a residual set whose size is user-defined. The model parameter uncertainties are included to prove the convergence of errors. Finally, a numerical example to validate the developed control is presented.