The purpose of this study was to investigate the antimicrobial activities of natural antimicrobials (10 formulas, F1~F10) against yeasts in functional beverages. The growth rates of yeasts were different with the ten different natural antimicrobial formulas tested. Yeasts grew for 14 days and the antimicrobial effect was observed between 14 and 18 days. Levels of S. cerevisiae, Z. bailii, and P. membranaefaciens were reduced to the limit of detection (ND) < 10 CFU/mL) after 28 days. Resistance against the antimicrobial effect was greatest for P. membranaefaciens, which grew to a level of 0.12~1.48 log10 CFU/mL after 14 days and was reduced to a level of 1.61~3.55 log10 CFU/mL after 28 days. The resistance of C. albicans was also high with a growth level of 0.13~1.28 log10 CFU/mL after 14 days and reduction to 1.51~5.30 log10 CFU/mL after 28 days. The antimicrobial effect of F10 was strongest for P. membranaefaciens. Every treatment reduced the microbial levels to 2.68~5.62 log10 CFU/mL after 6 months. F2, F4, F5, F6, and F10 reduced the C. albicans level to ND after 28 days while F1, F3, F8, and F9 reduced yeasts to the ND level after 6 months. The antimicrobial activities observed here will be useful for development of natural antimicrobials.