The microbial changes during thermophilic composting of food waste were investigated at 50 °C using a laboratory-scale composter. The results showed that an early increase in the growth of yeast was followed by the growth of thermophilic bacteria, and that subsequently, the yeast declined rapidly. The growth interactions of selected strains of yeast and bacteria were studied in culture media containing organic acids. The results demonstrated that the acidity of the media was reduced during the growth of the yeast. Therefore, it is concluded that in the early stages of composting, the growth of thermophilic bacteria is inhibited by organic acids, and that the growth of yeast enables subsequent bacterial growth by removing organic acids from food waste.