Influenza A virus (IAV) and Staphylococcus aureus (S. aureus) are important swine pathogens able to transmit via aerosol and with potential to affect human health. The electrostatic particle ionization system (EPI) is a technology able to reduce particles from the air and, as a result, it improves air quality and potentially the risk of pathogen spread. The objective of this study was to determine the effect of the EPI system on IAV and S. aureus in aerosols generated under experimental conditions. We also evaluated placing the EPI line at various distances to the ground and the effect of relative humidity (RH) on the system particle removal efficiency. Aerosols were generated artificially and sampled using both a cyclonic air sampler and an Andersen cascade impactor able to separate particles into different sizes. Air samples were collected with the EPI system “off” and “on” for 30 minutes with the EPI line connected at 1, 2 and 3 meters from the ground. Our results indicate that the EPI system was effective at reducing the levels of IAV and S. aureus found in the air. Under the conditions of this study, relative humidity did not affect the efficiency of the EPI system and reduction levels were greater for both pathogens when the EPI line was installed at 3 m from the ground which also corresponded to the closest distance to the aerosol source. In summary, the EPI system has potential to reduce exposure of zoonotic agents to producers and swine workers and improve the overall health and well being of pigs and people.