Present study evaluated the effect of effluent from submerged aerated biological filter (SABF) and activated sludge process (ASP) on the performance of membrane bioreactor (MBR). MBR was operated both in external configuration and internal configuration mode. Feeding SABF effluent to MBR resulted in a flux reduction of 2.3% and 12% under external and internal configurations, respectively. Volatile Organic Compound (VOC) removal from SABF effluent by MBR was only 13% in the external configuration mode whereas VOC was completely eliminated in the internal configuration mode. Treatment of effluent from ASP caused significant flux reduction and increase in transmembrane pressure (TMP) in the MBR. For both internal and external membrane configurations, substantial increase in extra cellular polymeric substances (EPS) and suspended solids resulted in higher membrane fouling during the treatment of ASP effluent. VOC removal from ASP effluent by MBR was achieved only while adopting internal configuration mode. Effective treatment of pharmaceutical wastewater, with less impact on membrane performance and reduced VOC emission to the atmosphere, can be achieved by coupling SABF with MBR and adopting internal configuration mode. © 2015 Published by Elsevier Ltd.