A biofilm is a three-dimensional microbial community, which is difficult to completely control with a typical sanitizer owing to its complex structure. The aim of this study was to establish a system for the combined treatment of biofilms with 10 ppmv gaseous chlorine dioxide (ClO2) and antimicrobial agents (2% citric acid, 2% hydrogen peroxide [H2O2], and 100 ppm peracetic acid [PAA]), and to investigate the synergistic microbicidal efficacy of the combination treatments to inactivate Listeria monocytogenes, Salmonella Typhimurium, and Escherichia coli O157:H7 in biofilms. The antimicrobial agents were aerosolized using a humidifier on top of a chamber to achieve a relative humidity of 90% (within a range of ±2%). While biofilm treatment with the aerosolized antimicrobial agents for 20 min inactivated approximately 1 log CFU/cm2 (0.72–1.26 log CFU/cm2) of the pathogens and the gaseous ClO2 gas treatment for 20 min inactivated <3 log CFU/cm2 (2.19–2.77 log CFU/cm2), combination treatment with citric acid, H2O2, and PAA for 20 min achieved microbial reductions of 2.71–3.79, 4.56–5.12, and 4.45–4.67 log CFU/cm2, respectively. Our study demonstrates that foodborne pathogens in biofilms can be inactivated by combining gaseous ClO2 treatment with aerosolized antimicrobial agents. The results of this study provide baseline data for the food industry to help control foodborne pathogens in biofilms on inaccessible surfaces.