A model for the numerical simulation of the action of microbioreactor acting in the continuous flow mode was developed. The microbioreactor system was mathematically modelled by a two-compartment model based on transient reaction-diffusion equations containing a non-linear term related to the Michaelis–Menten kinetics of the enzymatic reaction. The effectiveness of microbioreactor and the process duration were numerically and partially analytically analysed at transition and steady-state conditions in a wide range of model parameters. The computational simulation was carried out using the finite difference technique. The performed calculations showed nonlinear effects of the internal and external diffusion limitations on the effectiveness and process duration.