A microchannel reactor system was used in a biodesulfurization process in which the rate of biodesulfurization in the oil/water phase of the microchannel reaction was more than nine-fold that in a batch (control) reaction. In addition, the microchannel reaction system using a bacterial cell suspension degraded alkylated dibenzothiophene that was not degraded by the batch reaction system. This work provides a foundation for the application of a microchannel reactor system consisting of biological catalysts using an oil/water phase reaction.