Derived from RNA, 5ʹ-ribonucleotides, especially Inosine-5ʹ-monophosphate (IMP) and guanosine-5ʹ-monophosphate (GMP), can enhance the umami taste of soy sauce. In this study, the RNA content of three different salt-tolerant yeasts was examined. The most valuable strain was subjected to atmospheric and room-temperature plasma (ARTP) mutagenesis, which improved its RNA content by 160.54%. Regular fermentation with RNA-enhanced strain failed to increase the amount of 5ʹ-ribonucleotides in the soy sauce due to hydrolysis by phosphatase. A two-stage fermentation strategy was then carried out. Aroma compounds were mainly synthesized in the first stage, and RNA-enriched biomass was massively produced in the second stage followed by heat treatment to inactivate phosphatase. After the proposed strategy was applied, IMP and GMP in the soy sauce reached 68.54 and 89.37 mg/L, respectively. Moreover, the amounts of key aroma compounds and organic acids significantly increased. Results may provide new insights for improving the quality of soy sauce through microorganism breeding and fermentation control.