Biodesulfurization (BDS) in a bioreactor packed with a catalytic bed of silica containing immobilized Rhodococcus rhodochrous was studied. Various bed lengths and support particle sizes were evaluated for BDS of dibenzothiophene (DBT) and gas oil. The sulfur-containing substrates were introduced separately into the bioreactor at different feed flows. Higher removal of sulfur from DBT and gas oil was achieved with a long bed, lower substrate flow, and larger sizes of immobilization particles. The packed bed bioreactor containing metabolic active cells was recycled and maintained BDS activity.