To develop a new preservation method, the antimicrobial activity of grapefruit seed extract (GSE) against Makgeolli-brewing microorganisms and food-borne pathogens was assessed, and a general analysis and sensory evaluation of fresh Makgeolli with added GSE was made. The minimum inhibitory concentration (MIC) values of GSE against 10 strains of Makgeolli-brewing microorganism were 0.0122 to 1.5625 μL/mL. The MIC values against 6 strains of food-borne pathogens were 0.0061 to 0.7813 μL/mL. On addition of 0.1% (v/v) and 0.2% GSE in bottled fresh Makgeolli, no significant difference in the pH, or the contents of total acids, ethanol, or methanol in the Makgeolli, were observed compared with control Makgeolli (with no GSE), during the preservation period (8 weeks) at 10 °C. In the Makgeolli with 0.1% and 0.2% GSE, the total bacterial counts decreased significantly by 4.9% (P < 0.01) and 11.2% (P < 0.001), respectively, versus the control. The decreases in yeast count were significantly lessened by 15.33% and 15.24% (both P < 0.001), respectively, after 8 weeks of storage, compared with the control. In the sensory evaluation of Makgeolli with 0.1% and 0.2% GSE, the refreshment and overall acceptability received significantly better scores than the control (P < 0.01), with no change in sweetness, bitterness, sourness, turbidity, color, or odor. These results suggest that GSE controls the growth of Makgeolli-brewing microorganisms and extends the shelf life (ca. 2 wk), without decreasing overall acceptance. A new preservation method for fresh Makgeolli by adding grapefruit seed extract (GSE) was developed. As fresh Makgeolli contains live microorganisms, the preservation period is 1 wk, which is relatively short. GSE controls the growth of Makgeolli-brewing and Makgeolli-spoiling microorganisms. 0.1% to 0.2% GSE is optimum for prolonging the shelf life (2 wk) of bottled fresh Makgeolli, and has no adverse effect on overall acceptability. We demonstrated that GSE is an effective natural additive that prolongs the shelf life of fresh Makgeolli with no significant loss in quality.