Laboratory-scale experiments were performed to investigate the performance of the on-site small-scale combined system of membrane separation bioreactor (MSB) and zeolite-iron (Z-Fe) column. Average nitrogen removal by the membrane separation bioreactor was varied from 83% at an influent nitrogen concentration of 30 mg/l to 50% at 75 mg/l. Residual ammonia nitrogen in the effluent from the membrane separation bioreactor was further polished by a Z-Fe column to an initially non-detectable concentration and finally to 1.2 mg/l. The average phosphorus removal by this column unit was 70%. Improvement by providing aeration to the bottom part of iron bed in the long column improved phosphorus removal efficiency to as much as 92% until water logging occurred inside the column. Moreover, further improvement was achieved by inserting three short columns in series for 116 day of operation. Average effluent phosphorus concentrations of 1.2, 0.39 and 0.16 mg/l were obtained after the 1st, 2nd and 3rd column respectively with an applied influent phosphorus concentration of 5.3 mg/l on average. Furthermore, batch experiments were carried out to investigate the factors, such as pH and temperature, which affect the performance of the Z-Fe column in phosphorus removal.