We investigated the possibility of applying performic acid (PFA) and peracetic acid (PAA) for disinfection of combined sewer overflow (CSO) in existing CSO management infrastructures. The disinfection power of PFA and PAA towards Escherichia coli (E. coli) and Enterococcus were studied in batch-scale and pre-field experiments. In the batch-scale experiment, 2.5 mg•L-1 PAA removed approximately 4 log unit of E. coli and Enterococcus from CSO with a 360 min contact time. The removal of E. coli and Enterococcus from CSO was always around or above 3 log units using 2–4 mg•L-1 PFA; with a 20 min contact time in both batch-scale and pre-field experiments. There were no toxicological effect measured by Vibrio fischeri when CSO was disinfected with PFA, a slight toxic effect was observed on CSO disinfected with PAA. When the design for PFA based disinfection was applied to CSO collected from an authentic event, the disinfection efficiencies were confirmed and degradation rates were slightly higher than predicted in simulated CSO.