To study the effect of natural anti-microbial chemicals on the growth and quality of chili peppers, chitosan (100 mg/L), stevia (250 mg/L), and the mixture of both chemicals at the same concentration were sprayed after planting at 1-week interval throughout the experimental period. Plant height was measured twice after the 3 and 4 applications. Plant height was numerically reduced in all chemical treatments compared to that of untreated control; however, there was no statistical difference between treatments. The fruit quality was examined at commercial maturity, and only minor differences were found in fruit color, length, and dry matter content between the treatments. Although a statistical difference was not present for soluble sugars levels, total phenolics, and capsaicin contents, yield in all chemical treatments significantly increased compared to untreated control. The effect on yield increase was greater at the late harvest season regardless of treatments. Total yield of 4 harvests was higher for the chitosan treatment than other treatments. During the experiment, the entire experimental field was waterlogged for 1 day due to sudden heavy rainfall, which resulted in the occurrence of bacterial browning disease in all treatments. The rate of disease occurrence and the degree of severity, however, were much lower in the chitosan treatment. In conclusion, the potential of chitosan as an alternative antimicrobial agent was confirmed in chili peppers in this study. Further research is required on stevia as an alternative chemical for disease control in chili peppers.