Environmental risk allopathically concern on antibiotics is rising due to their low degradability, biotoxicity, and so on. In this study, wastewater containing ammonium and selected antibiotics (Tetracycline (TC), Sulfamethoxazole (SMX) and Ampicillin (AMP)) was used as influent. A lab-scale conventional anoxic/aerobic membrane bioreactor (A/O-MBR) and a A/O-MBR with immobilized beads (I-A/O-MBR) were operated in parallel in order to carry out a direct comparison in terms of selected antibiotics and other pollutants removal efficiencies. The results showed that the removal efficiencies of TC, SMX, and AMP were above 90%, 95%, and 99% respectively in A/O-MBR, and the removal efficiencies were kept stable in different phases. But TOC, NH4+-N and TN removal rate were significantly impacted with the antibiotics loading fluctuating. Most of the antibiotics can be removed in A/O-MBR process under different influent conditions, whereas efficiencies of other pollutants may be affected with the fluctuating of pollutants concentration in influent. Poor adsorption ability, low contacting area between immobilized bacteria and wastewater were considered as key factors for I-A/O-MBR process which led to lower antibiotics removal efficiencies than in the A/O-MBR process. While protection effect of immobilized beads on the antimicrobial activity could ensure good performance and stability on conventional pollutants removal.