Development of "green" multi-functional air filters with features such as excellent filtration efficiency, eco-friendliness, and environmental stability are critically required to address the increasing concerns of polluted air. Natural proteins, such as soy protein and gelatin, are attractive candidates as multi-functional air-filtration materials owing to the rich functional groups; however, these bio-materials are vulnerable to moisture, which limits their broad application in practice. In this work, a hydrophobic protein of zein derived from abundant corn is modified for the first time to produce high-performance nanofilters via electrospinning. The zein nanofabrics are fabricated with the aid of a non-toxic solvent and co-electrospinning agent, poly(ethylene oxide). The results reveal that the zein-based nanofabrics show high efficiency for the simultaneous removal of particulate matters of different sizes ranging from 0.1 to 10 μm (> 99.5%) and certain gaseous toxic chemicals (> 70%). In addition, the zein nanofabrics show excellent moisture-resistance and good adhesion to the cellulose paper towel used as the air-filter substrate. This study demonstrates that nanofabrics based on hydrophobic natural proteins such as zein are promising materials for developing multi-functional "green" air filters.