Various pathogenic microorganisms present in municipal solid waste (MSW) can pose significant hazards to both the environment and public health. Spraying Slightly Acidic Electrolyzed Water (SAEW) is an effective method for decontaminating microorganisms in the air and on surfaces in the waste sorting rooms. SAEW treatment, with an effective chlorine concentration (ECC) of 28.4–44.5 mg/L and a pH range of 5.0–6.5, was conducted in the waste sorting rooms of the old, high-rise, and villa residential communities in Shanghai, China. The efficacy of SAEW treatment was assessed by examining the microbial population in the air, on waste containers, on sanitation workers' hands, and the microbial community structure of MSW samples. SAEW treatment resulted in the total bacterial reduction ranging from 0.07 to 1.70 log10 colony-forming units (CFU)/cm2 on waste containers, with corresponding reduction efficiencies between 15.7% and 98.0%. Additionally, the positive rates of coliforms were decreased by 18.7%–95.2%. Furthermore, the application of SAEW demonstrated a significant impact on reducing airborne bacterial and fungal levels. SAEW was proven effective on object surfaces, in the air and on human skin, achieving disinfection efficiencies ranging from 22.7% to 54.3% on sanitation workers’ hands. And the most significant inhibition of microbial growth was observed in the waste sorting room of the villa residential community. The microbial diversity and structure of MSW samples exhibited noticeable differences before and after the SAEW application. These findings suggest that SAEW holds significant potential as an ideal, environmentally friendly broad-spectrum disinfectant for preventing and controlling microbial contamination in the waste sorting rooms.