In this study, any remaining nitrate not eliminated during a biological treatment process with a low C/N ratio was effectively removed using sulfur powder in an autotrophic denitrification membrane bioreactor. Moreover, particular attention was given to investigating the potential for membrane fouling in a sulfur-based denitrification reactor, with a comparative analysis to conventional activated sludge in an aerobic membrane bioreactor. At an influent nitrate concentration of 320 mg/L, the removal efficiency reached 94–98 % within a 4-hour hydraulic retention time and at a reactor temperature of 30 °C. The sulfur-based denitrification reactor exhibited soluble microbial products concentration and specific cake resistance values of 38.3 mg/L and 1.4 × 1013 m/kg, respectively, which were 5.47 and 2.26 times higher than those of conventional activated sludge. Furthermore, it was observed that the supernatant from the sulfur-based denitrification reactor resulted in more significant fouling within the membrane surface.