A membrane enzymatic reactor, consisting of a stirred tank coupled to an ultrafiltration membrane was set up for the enzymatic oxidation of xenobiotic compounds. The azo dye Orange II was selected for the model compound and manganese peroxidase for the oxidative enzyme. The ligninolytic cycle was initiated and maintained by the controlled addition of all factors (reactants, mediators, and stabilizers) at suitable rates. Considering the distinctiveness of this process, in which the substrate to be oxidized is not the primary substrate for the enzyme, a kinetic model was developed. The azo dye concentration and hydrogen peroxide addition rate were found to be the main factors affecting the process. The reaction kinetics was defined using a Michaelis-Menten model with respect to the Orange II concentration and a first-order linear dependence relative to the H2O2 addition rate. The dynamic model, which takes into account both the kinetics and the hydraulics of the system, was validated by comparing the experimental results in continuous operation under steady and non-steady state to model predictions. In particular, the model predicted the behavior of the system when unexpected alterations in steady-state operation occurred. Furthermore, the model allowed us to obtain the most appropriate H2O2/Orange II ratio in the feed to maximize the process efficiency.