This study investigated the interactions of four bacteria strains isolated from Yamahai-shubo, the source of yeast used to produce a Japanese traditional rice wine, Yamahai-shikomi sake. The bacterial strains were nitrate-reducing Pseudomonas sp. 61-02, Leuconostoc mesenteroides LM-1, Lactiplantibacillus plantarum LP-2, and Latilactobacillus sakei LS-4. We examined fermentation factors for Yamahai-shubo and Yamahai-shikomi sake samples to compare the suitability of their bacterial combination (16 variations). As a result of principal component analysis, we found that two major groups were formed; one containing strain LP-2 and the other containing strain LS-4, and that strains LP-2 and LS-4 were important in the Yamahai-shikomi sake in the presence of strains 61-02 and LM-1. Then, we investigated the effects of strains LP-2 and LS-4 on the concentration of organic acids (pyruvic acid, citric acid, succinic acid, malic acid, and lactic acid) in Yamahai-shikomi sake. Only in lactic acid, a tendency to decrease with a smaller proportion of LS-4 strains in Yamahai-shubo was observed. Subsequently, their effect on the concentration of diacetyl, crucial for aroma, was investigated between the LP-2 and LS-4 strains. The sample prepared in the absence of strain LS-4 exhibited the lowest concentration of diacetyl. This result was supported by the statistical analysis for the sensory scores performed for aroma of each Yamahai-shikomi sake sample. In conclusion, strain LP-2 plays a more significant role in improving Yamahai-shikomi sake quality with strains LM-1 and 61-02 rather than strain LS-4 in Yamahai-shubo preparation and Yamahai-shikomi sake brewing.