Wastewater disinfection is important to protect human and ecosystem health. Peracetic acid (PAA) could be used as a disinfectant for wastewater and has the advantage of being less toxic to aquatic species and forming fewer known disinfection byproducts than traditionally used chlorine. Assessment of the relative performance of PAA and chlorine at different exposures and seasonal temperatures is still needed to promote utility adoption especially in cold environments and for non-traditional applications such as water reuse. Additionally, the combination of PAA and UV disinfection has the potential to augment inactivation especially against more resistant microorganisms. In this study, the disinfection efficiency of PAA and chlorine was compared for four microorganisms: two fecal indicator bacteria (E. coli and Enterococcus spp.), a virus (somatic coliphage), and a protozoan (Cryptosporidium parvum). Experiments were conducted in authentic secondary wastewater samples to compare PAA and NaOCl disinfection at two C·t values (20 mg min l⁻¹ and 60 mg min l⁻¹) and two temperatures (room temperature and 4 °C), investigate combined PAA plus UV treatment, and evaluate PAA and PAA plus UV disinfection after 10 min and 24 h. PAA and NaOCl disinfection efficiency was comparable for E. coli, Enterococcus spp. and somatic coliphage at a C·t of 60 mg min l⁻¹ (2 mg l⁻¹, 30 min) but not at 20 mg min l⁻¹ (2 mg l⁻¹, 10 min). Neither PAA nor NaOCl disinfection reduced concentrations of Cryptosporidium parvum oocysts spiked into secondary wastewater. At a winter-relevant temperature (4 °C), NaOCl was more effective against E. coli and Enterococcus spp. than PAA regardless of exposure, while both PAA and NaOCl achieved comparable somatic coliphage inactivation. The combined use of PAA and UV treatment appear to have achieved higher log reductions than the use of PAA only for E. coli and somatic coliphage, and of UV only for E. coli. Log reductions after PAA and PAA plus UV treatments continued to increase up to 24 h after exposure which has implications for distribution systems for reclaimed water used for irrigation purposes. The results presented here support the use of PAA as an alternative wastewater disinfectant to chlorine and as a complimentary disinfectant to UV.