Performic acid (PFA) has gained interest as an alternative chemical disinfectant for wastewater (WW) treatment, but its reactivity with WW constituents remains poorly understood. This study evaluated PFA’s ability to oxidize 45 inorganic and organic compounds commonly found in WW (amino acids, simple organic compounds with specific functional groups, e.g., amines and phenolic compounds, and pharmaceutical micropollutants). PFA does not react with most major ions, except for iodide ions, and reacts with iron(II) in the absence of phosphate buffer. While many organic molecules do not react with PFA, compounds containing reduced-sulfur moieties (e.g., thioether or thiol) are the most reactive (i.e., ranitidine, benzenethiol, and 3-mercaptophenol), followed by compounds with tertiary amine groups (e.g., lidocaine). The reactions follow second-order kinetics with respect to both organic compounds and PFA concentrations. Similar trends were observed in real WW effluents, although removals of pharmaceuticals were lower than expected due to the probable consumption of PFA by WW constituents (dissolved organic carbon, other micropollutants, or transition metals). The results highlight PFA’s selective reactivity with specific functional groups and a low transformation of compounds mostly through oxygen addition (e.g., S-oxide or sulfonyl compounds formed from thiol and thioether moieties and N-oxides from amine groups) with similar mechanisms to peracetic acid.