This study introduces natural occurring magnetic pyrrhotite (NP) as an environmentally friendly, easy available, and cost-effective alternative catalyst to activate persulfate (PS) of controlling microbial water contaminants. The E. coli K-12 inactivation kinetics observed in batch experiments was well described with first-order reaction. The optimum inactivation rate (k = 0.47 log/min) attained at a NP dose of 1 g/L and a PS dose of 1 mM, corresponding to total inactivation of 7 log10 cfu/mL cells within 15 min. Measured k increased > 2-fold when temperature increased from 20 to 50 °C; and > 4-fold when pH decreased from 9 to 3. Aerobic conditions were more beneficial to cell inactivation than anaerobic conditions due to more reactive oxygen species (ROS) generated. ROS responsible for the inactivation were identified to be SO4− > OH > H2O2 based on a positive scavenging test and in situ ROS determination. In situ characterization suggested that PS effectively bind to NP surface was likely to form charge transfer complex (≡Fe(II)⋯O3SOOSO3-), which mediated ROS generation and E. coli K-12 oxidation. The increased cell-envelope lesions consequently aggravated intracellular protein depletion and genome damage to cause definite bacterial death. The NP still maintained good physiochemical structure and stable activity even after 4 cycle. Moreover, NP/PS system also exhibited good E. coli K-12 inactivation efficiency in authentic water matrices like surface water and effluents of secondary wastewater.