Disinfection with performic acid (PFA) represents an emerging technology in wastewater treatment. Many recent studies indicate its effectiveness and suitability as a disinfectant for different applications; several have demonstrated its reliability as an alternative to chlorine for disinfecting secondary effluents from urban wastewater treatment plants (WWTPs). Some disinfection technologies, in relation to their oxidative power, lead to the formation of disinfection by-products (DBPs), some of which are of concern for their toxic and carcinogenic potential. The aim of this study was to investigate potential genotoxic, cytotoxic, and mutagenic effects of this disinfection agent on treated secondary effluent coming from a municipal WWTP. A strategy with multiple short-term tests and different target cells (bacterial, plant, and mammalian) was adopted to explore a relatively wide range of potential genotoxic events. The Ames test (point mutation in Salmonella), the micronucleus (chromosomal damage) and Comet tests (primary DNA damage) on human hepatic cells (HepG2) were conducted to detect mutagenicity and chromosomal DNA alterations. DNA fragmentation and mitochondrial potential assays were conducted to evaluate apoptosis in the same kinds of cells. Mutagenic and clastogenic effect potentials were evaluated by examining micronucleus formation in Allium cepa root cells. In all the in vitro tests, carried out on both disinfected and non-disinfected effluents, negative results were always obtained for mutagenic and genotoxic effects. In the Allium cepa tests, however, some non-concentrated wastewater samples after PFA treatment induced a slight increase in micronucleus frequencies in root cells, but not in a dose-related manner. In conclusion, PFA applied for disinfection to a secondary effluent from a municipal wastewater treatment plant did not contribute to the release of genotoxic or mutagenic compounds. Further studies are required to establish to which extent these findings can be generalized to support PFA for other disinfection applications.