Few studies have focused on the feasibility of microbial fuel cells (MFCs) for removing quinolones antibiotics and their anti-shock capabilities. After 1.5 years of operation, the removal efficiency of 10 mg/L ciprofloxacin in MFCs increased to 99.00% in 88 h. These results are in accordance with the enhanced activity of biofilms and voltage output of MFCs. Additionally, the anti-shock capacities of the biofilms in MFCs were evaluated by treating ofloxacin and enrofloxacin and operating at different temperature and salinity. These MFCs can remove 87.31% and 40.81% of ofloxacin and enrofloxacin in 72 h, respectively. Even exposed to a low temperature of 10 °C or a salinity of 3%, the MFCs can achieve greater than 50% and nearly 80% of ciprofloxacin removal efficiency, respectively. The enrichment of Alcaligenes and Chryseobacterium contributed mostly to the removal of quinolones antibiotics. This study provides scientific evidences for treating wastewater containing quinolones antibiotics using MFCs.