Makgeolli mashes that were brewed using five different commercial nuruks (fermentation starters) were investigated for changes in physicochemistry, microbial diversity, and biogenic amine (BA) production. Mash A brewed with the nuruk (Gaeryang-nuruk) had the highest level of alcohol concentration and the greatest number of yeast cells, whereas mash E had the greatest number of bacterial cells. Only three biogenic amines were detected in the makgeolli mashes: tyramine, putrescine, and cadaverine. Using a PCR-DGGE technique, we observed that mash E had the highest BA production, and had the greatest number of bands on the denaturing gradient gels. We also observed that the numbers of bacterial cells correlated significantly with the putrescine and the total BA content, and that the BA content correlated significantly with the color values (L, a, b). This study shows that the quality of a makgeolli can depend on the type of nuruk. Therefore, we suggest that the quality management of makgeolli should start with the stage of nuruk manufacture.