A double membrane system combining a membrane bioreactor (MBR) with a nanofiltration (NF) membrane at the pilot scale was tested to treat real antibiotic wastewater at a pharmaceutical company in Wuxi (China). The water yield of the pilot system reached over 92 ± 5.6% through recycling the NF concentrate to the MBR tank. Results showed that the pilot scale system operated in good conditions throughout the entire experiment period and obtained excellent water quality in which the concentrations of chemical oxygen demand and total organic carbon were stable at 35 and 5.7 mg/L, respectively. The antibiotic removal rates of both spiramycin (SPM) and new spiramycin in wastewater were over 95%. Organics analysis results showed that the main organics in the biological effluent were proteins, soluble microbial by-product-like, fulvic acid-like and humic-like substances. These organics could be perfectly rejected by the NF membrane. Most of the organics could be removed through recycling NF concentrate to the MBR tank and only a small part was discharged with NF concentrate and permeate.