The application of grapefruit seed extract (GSE) and air ions to filters was investigated with the goal of collecting indoor bioaerosols. GSE exhibits antimicrobial activity because it contains flavonoids such as naringin. Air ions are usually generated by electric ionizers and can inactivate bacteria, viruses, and fungi. In this study, GSE particles were coated onto three different filters: polypropylene (PP), activated carbon fiber (ACF), and metal foam (MF). Ions were supplied to the filter surface using an ionizer. The rate of surface inactivation of Staphylococcus aureus was measured. When only GSE was applied to the filters, the inactivation rate was about 60%; when air ions were applied, the rate was about 70–80%. When both GSE and ions were applied simultaneously, the inactivation rate increased to 80–90%. The physical collection efficiencies of the as-purchased filters were in the following order: PP > ACF > MF. However, when ions were supplied to the filters, the collection efficiencies increased to over 98% for each filter. The inactivation rate of the ACF filter was the highest (92.5%). Therefore, we conclude that the ACF filter is the most efficient of these three filters for inactivating S. aureus.