Microbial contamination is the major safety concern of sprouts, and its main source is the seeds. Achieving effective reduction requires very high concentrations of chlorine-based disinfectants (>10,000 mg/kg). Thus, the objective of this study was to combine microbubble (MB) with chlorine dioxide (ClO2, 500 mg/L) and slightly acidic electrolyzed water (SAEW, containing 250 mg/L of available chlorine) to inactivate Salmonella Typhimurium on mung bean seeds. MB water containing disinfectants (10 L) was generated for 10 min, then the seeds were treated for 10, 20, or 30 min. Significant reductions were obtained by combining MB with disinfectants. After 20-min treatment, ClO2-MB (ClMB) achieved additional reductions of 3.7 and 2.3 log CFU/g, respectively, compared with water washing and ClO2 only. SAEW-MB (SMB) achieved additional reductions of 3.6 and 2.0 CFU/g, respectively when compared with water washing and SAEW only after 20-min treatment. No significant difference for the reduction in S. Typhimurium was observed (p ≥ 0.05) between 20-min and 30-min treatments, but increased damage to seeds was evident after 30-min treatment. More surface cracks were observed on the seeds treated with ClMB than on those subjected to water washing and ClO2 only when examined under a scanning electron microscope. However, the germination rate of seeds and the weight increase of sprouts were not significantly different between treatments of ClMB, water washing, and ClO2 only. A large-volume MB device (100 L) was established, resulting in a reduction of S. Typhimurium and natural microflora by 3.1 and 3.3 log CFU/g, respectively, after a 20-min ClMB treatment. This study's findings demonstrated how MB enhances the effectiveness of disinfectants and its potential capacity for large-scale operation.