In the current COVID‐19 pandemic, wearing masks and hand disinfection are widely adopted hygiene practices. Alcohol‐based sanitizers are commonly used for hand disinfection, however, the alcohol vapors can dissipate the charges on electrostatic filters. In the present study, the effects of alcohol vapors from alcohol‐based sanitizers during hand disinfection on the in‐use masks are studied. The results show that the negative effects are not significant for nonelectrostatic cotton masks or N95 respirators with multiple charged layers, but noticeable for surgical masks. After five rounds of hand disinfection, the filtration efficiencies of the filtering materials of the surgical masks decrease by more than 8% for 400 and 500 nm particles and by 3.7 ± 1.8% for 1 µm particles, the effective filtration efficiency of the surgical masks worn by the volunteers (with leakage considered) decreases by about 5% for ambient aerosol. In another process to imitate intensive disinfection procedures by healthcare workers, a 30 min surface cleaning process using alcohol‐based sanitizer is performed, and the effective efficiency of the N95 respirators worn by the volunteers decreases by nearly 9%. The simple practice of avoiding vapor during hand disinfection could mitigate the effects of alcohol vapor, which is demonstrated on two brands of surgical masks.