Display omitted •Ciprofloxacin affected treatment performance and fouling propensity of Sponge-MBR.•COD removal was 94–98% under the added CIP dosage less than 100 µg L−1.•High CIP dosages enhanced nitrification but significantly inhibited denitrification.•Floc size and membrane fouling decreased at high CIP dosages of 100–200 µg L−1. This study aimed to evaluate treatment performance and membrane fouling of a lab-scale Sponge-MBR under the added ciprofloxacin (CIP) dosages (20; 50; 100 and 200 µg L−1) treating hospital wastewater. The results showed that Sponge-MBR exhibited effective removal of COD (94–98%) during the operation period despite increment of CIP concentrations from 20 to 200 µg L−1. The applied CIP dosage of 200 µg L−1 caused an inhibition of microorganisms in sponges, i.e. significant reduction of the attached biomass and a decrease in the size of suspended flocs. Moreover, this led to deteriorating the denitrification rate to 3–12% compared to 35% at the other lower CIP dosages. Importantly, Sponge-MBR reinforced the stability of CIP removal at various added CIP dosages (permeate of below 13 µg L−1). Additionally, the fouling rate at CIP dosage of 200 µg L−1 was 30.6 times lower compared to the control condition (no added CIP dosage).