BACKGROUND: The operation of a high-rate anaerobic process usually suffers from problems of high sensitivity to disturbances arising from environmental and operational factors. Application of advanced process controls is an efficient approach to enhancing process robustness and stability. RESULTS: A multivariable linear quadratic tracking (LQT) approach to the output tracking of an anaerobic reactor was proposed, using external recirculation-to-feed ratio (R-s) and external bypass-to-feed ratio (R-r). The anaerobic digestion process is described by a distributed parameter model with a two-step (acidogenesis-methanization) kinetics. A state space model was developed using linear approximations of the nonlinear terms, and an output tracking method was developed combining linear quadratic tracking (LQT) and an integral action. CONCLUSION: Simulations show that, compared with the normal LQT method and proportional-integral (PI) controller, using both R-r and R-s and a conventional dilution rate (D,) based single variable PI controller, the proposed control approach achieved better results in both output set-point tracking and stabilization of effluent quality under influent disturbances and model-process mismatch. The new control strategy also had the advantage of using less storage capacity. (c) 2008 Society of Chemical Industry.