The purpose of this study was to evaluate the effect of air-bubble washing with natural sanitizers on microbial contamination such as aerobic bacteria, yeast, and mold, and the quality characteristics of perilla seeds. Bubble washing was more effective than immersion washing for all washing times. The microorganism counts decreased as a function of bubble washing time, with an optimum air-bubble washing time of 60 min. In addition, immersion and bubble washing with natural sanitizers such as vinegar and brine of 1, 2.5, and 5% caused a dramatic decrease in the microorganism counts compared with washing without sanitizers. There was no significant difference between 2.5% and 5% vinegar in bubble washing efficacy. The results of bubble washing with brine were similar to those of bubble washing with vinegar, but vinegar resulted in more effective microbial decontamination than brine at all concetrations. In addition, bubble washing with vinegar and brine did not alter the oxidative stability of perilla seeds as determined by acid and peroxide values. As a result, air-bubble washing with natural sanitizers is an effective method to reduce the microbial contamination and enhance the microbiological safety of perilla seeds.