In this study, the interaction of the magnetotactic bacterium with sulfite compounds and their potential to degrade SO2 was investigated using cyclic voltammetry (CV), molecular emission cavity analysis (MECA) and ion-exchange chromatography (IEC). This biofilter was able to degrade SO2 up to 22281 mg m−3 by disproportionation reaction and the formation of S2− and SO42− with ≥99% efficiency. Designed biofilter was able to restart the initial performance at least after seven cycles if it was used at 14-day intervals. According to theoretical studies, the value of mean free energy (E) obtained using the Dubinin-Radushkevich isotherm model was 0.02 kJ mol−1, which is in the range expected for physical adsorption. Designed biofilter can be considered as a powerful tool to degrade SO2 in diverse urban and industrial centers.