This study developed a novel antimicrobial air filter by functionalizing polypropylene nonwoven fabrics with bovine lactoferrin peptide to control indoor bioaerosols. The filtration performance was evaluated against E. coli and virus under various environmental conditions. Results demonstrated broad-spectrum inactivation efficacy, with the 2.0 mg coating achieving the highest performance in a dose-dependent manner. A critical breakthrough was the environmental stability of the lactoferrin coating; unlike traditional biopolymers, its antimicrobial efficiency remained consistent across 30–70% relative humidity (p > 0.05). Furthermore, a field test conducted in a dental clinic validated its practical feasibility, achieving an 83.3% reduction in bacterial bioaerosols over a 210-min operation. These findings suggest that lactoferrin-functionalized filters offer a robust, moisture-resistant, and safe solution for improving indoor air quality in high-risk environments.