Performic acid (PFA) has been increasingly used in wastewater disinfection due to its strong oxidizing ability and few disinfection byproducts. However, its disinfection pathways and mechanisms towards pathogenic bacteria disinfection are poorly understood. In this study, E. coli, S. aureus, and B. subtilis were inactivated using sodium hypochlorite (NaClO), PFA, and peracetic acid (PAA) in simulated turbid water and municipal secondary effluent. Cell culture-based plate counting showed that E. coli and S. aureus were extremely susceptible to NaClO and PFA and achieved a 4-log inactivation at CTs ≤ 1 mg/L·min with an initial disinfectant concentration of 0.3 mg/L. B. subtilis was much more resistant. At the initial disinfectant dose of 7.5 mg/L, PFA required CTs of 3-13 mg/L·min to achieve a 4-log inactivation. Turbidity negatively affected the disinfection. In the secondary effluent, the CTs required for PFA to achieve a 4-log inactivation of E. coli and B. subtilis were 6-12 times higher than those required in simulated turbid water, and a 4-log inactivation of S. aureus could not be achieved. PAA showed a much weaker disinfection ability than the other two disinfectants. The reaction pathways of E. coli inactivation by PFA included both direct and indirect reactions, in which the PFA molecule accounted for 73 %, and ·OH and peroxide radicals accounted for 20 % and 6 %, respectively. During PFA disinfection, E. coli cells were severely disintegrated, while the S. aureus cell exteriors remained mostly intact. B. subtilis was the least affected. Compared with cell culture-based analysis, the inactivation detected by flow cytometry was significantly lower. Viable but non-culturable bacteria after disinfection were believed to be primarily responsible for this inconsistency. This study suggested that PFA was able to control regular bacteria in wastewater, but it should be used with caution when treating recalcitrant pathogens.