Incomplete mineralization of antibiotics in biological sludge systems poses a risk to the environment. In this study, the toxicity associated with ciprofloxacin (CIP) biodegradation in activated sludge (AS), anaerobic methanogenic sludge (AnMS), and sulfur-mediated sludge (SmS) systems was examined via long-term bioreactor tests and a series of bioassays. The AS and AnMS systems were susceptible to CIP and its biotransformation products (TPs) and exhibited performance deterioration, while the SmS system exhibited high tolerance against the toxicity of CIP and its TPs along with excellent pollutant removal. Up to 14 TPs were formed via piperazinyl substituent cleavage, defluorination, decarboxylation, acetylation, and hydroxylation reactions in AS, AnMS, and SmS systems. Biodegradation of CIP in the AS, AnMS, and SmS systems, however, could not completely eliminate its toxicity as evident from the inhibition of Vibrio fischeri luminescence along with Escherichia coli K12 and Bacillus subtilis growth. The anaerobic systems (AnMS and SmS) were more effective than the aerobic AS system at CIP biodegradation, significantly reducing the antibacterial activity of CIP and its TPs in the aqueous phase. In addition, the quantitative structure-activity relationship analysis indicated that the TPs produced via decarboxylation and hydroxylation (TP2 and TP4) as well as by cleavage of piperazine (TP12, TP13, and TP14) exhibited higher toxicity than CIP. The findings of this study provide insights into the toxicity and possible risks associated with CIP biodegradation in biological wastewater treatment.