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Peracetic acid (PAA) is being considered as a disinfectant in membrane-based wastewater reuse systems, but its compatibility with polyamide membranes has not been thoroughly investigated. In this work, we showed that PAA induced much less change in the performance and material characteristics of NF90 membranes than the traditional disinfectant free chlorine (NaOCl). The change in membrane water flux and the rejection of salt and neutral organic compounds after PAA exposure (1–180 g h L −1 ) is significantly less than that resulting from NaOCl exposure at levels as low as 1 g h L −1 . The presence of two wastewater constituents, chloride or Fe( ii ), did not significantly impact membrane performance upon exposure to PAA. Surface characterization showed that oxygen was incorporated into polyamide by PAA, some of which was attributed to the formation of carboxylic acid groups. Experiments using a model aromatic amide, benzanilide, indicated an unexpected role of PAA in protecting the membrane from radicals formed by Fe( ii ) and the H 2 O 2 present in commercial PAA formulations. Furthermore, product identification suggests that both amide bond breakage and ring oxidation are possible reaction mechanisms for PAA. Our findings support that PAA is a viable disinfectant candidate for wastewater reuse and warrants further evaluation.