Low condition of dissolved oxygen (DO) is commonly associated with sludge bulking problem that was able to disrupt the efficiency of wastewater treatment performances. Relatively, very little attention was paid to the possibility of applying magnetic field in controlling the bulking problem. Hence, this study aims to investigate the performance of magnetic field on biomass properties and its effect on biodegradation under low condition of DO. Two continuous laboratory-scale sequencing batch reactors—Reactor A (SBRA) and Reactor B (SBRB)—were setup. SBRA was equipped with the magnetic device to exhibit magnetic field of 88 mT, while SBRB acted as a control system. The results showed that the biomass concentration in SBRA was higher compared to SBRB. High biomass concentration in SBRA resulted to better settleability with mean SVI of less than 30 mL/g. SBRA also showed consistently high removal performances of organic and inorganic contents compared to SBRB. These observations confirmed that the magnetic field was able to enhance the biomass properties, which further enhance the biodegradation ability of the aerobic bacteria under low DO condition. This also indicates that under the sludge bulking circumstances, the use of magnetic field stands a great chance in maintaining high biodegradation of the treatment system.