The continuous ethyl acetate extraction of progesterone and 11alpha-hydroxyprogesterone, a reactant and the product of the biotransformation step involved in corticosteroid production, was studied in a microchannel at different flow velocities. In addition, non-steady state batch extraction without mixing was performed and modelled in order to verify the theoretically predicted parameters. In order to analyze experimental data and to forecast microreactor performance, a three-dimensional mathematical model with convection and diffusion terms was developed considering the velocity profile for laminar flow of two parallel phases in a microchannel at steady-state conditions. For the numerical solution of a complex equation system, non-equidistant finite differences were used. Very good agreement between model calculations and experimental data was achieved without any fitting procedure. Due to the efficient phase separation and high extraction yields obtained, the micro scale extraction units were found to be a promising tool for the development of an integrated system of 11alpha-hydroxylation of progesterone by Rhizopus nigricans in the form of pellets.