The disinfection of wastewater is a treatment that allows for its reuse. However, not all pathogenic microorganisms or their resistant structures, e.g., endospores, cysts, or oocysts, are eliminated in conventional treatments. This work compared the removal efficacy of sodium hypochlorite (NaClO) and peracetic acid (PAA) on three strains of bacteria isolated from the tertiary effluent of a wastewater treatment plant. The results of the inactivation kinetics showed that complete inactivation of S. pasteuri was achieved with both NaClO (>12 log, t = 5–10 min, 15–30 mg/L) and PAA (~9 log, t = 20–30 min, 15 mg/L). Likewise, with higher concentration of both disinfectants, the inactivation time decreased. K. pneumoniae showed greater resistance to PAA (3 log, t = 30 min) than to NaClO (8 log, t = 15 min). B. subtilis endospores showed resistance to NaClO (3 log, t = 60–100 min, 15 mg/L); however, PAA was more effective (~4 log, t = 45–100 min), with 15 mg/L regarding these latter four kinetics. The inactivation curves of these strains showed concave and linear tendencies with tail effects, fitting the Weibull and Geeraerd models. Both the inactivation kinetics and the models established for vegetative cells and endospores in this study are conclusive to understand the differences between these biological forms and, consequently, their ability to survive disinfection.