Peracetic acid (PAA) is an alternative disinfectant that may be effective for combined sewer overflow (CSO) disinfection, but little is known about the effect of particle size on PAA disinfection efficiency. In this work, PAA and hypochlorite were compared as disinfectants, with a focus on the effect of wastewater particles. Inactivation experiments were conducted on suspended cultures of Escherichia coli and wastewater suspended solids. Tested size fractions included particle diameters < 10 μm, < 100 μm, and raw wastewater. Chlorine disinfection efficiency decreased with increasing solids size. However, solids size had little effect on PAA disinfection. The PAA disinfection efficiency decreased at pH values above 7.5. Live/dead staining revealed that PAA disinfection leaves most cells in a viable but non-culturable condition. Fourier transform infrared spectroscopy (FTIR) analyses suggests that PAA and hypochlorite may inactivate E. coli bacteria by similar mechanisms.