This paper deals with the design and application of a nonlinear multivariable controller in an anaerobic digestion system (AD) carried out in two interconnected fixed bed bioreactors. The proposed control scheme is derived from a mathematical model of the AD system described by a set of partial differential equations and consists of an estimator and two nonlinear control laws. The first law is developed to regulate the volatile fatty acids in the first bioreactor while the second aims at maintaining the chemical oxygen demand at predetermined set-points in the second bioreactor. The performance of the control algorithm is evaluated via numerical simulations in the face of load disturbances, parameter kinetic uncertainties and set-point changes. Stability and convergence properties of the proposed control scheme are also addressed in this paper. (C) 2009 Elsevier Ltd. All rights reserved.