The aim of this study was to develop a bacteriocin-producing QPS (Qualified Presumption of Safety) status Bacillus strain as a starter culture for fermented soybean foods as well as food preservation with improved safety and organoleptic qualities. Strain SN7 isolated from Meju, a fermented soybean product of Korea, was selected based on antimicrobial activity against pathogens such as B. cereus and production of bacteriocin. The selected strain SN7 was identified as B. subtilis. Safety assessments of B. subtilis SN7 (hemolytic activity, virulence traits, and antibiotic resistance) indicated that B. subtilis SN7 does not present a risk to human health, and this new isolate can be confidently recommended as a safe starter culture for the food industry. Cheonggukjang, a traditional fermented soybean food of Korea, fermented using B. subtilis SN7 showed high amino-type nitrogen content with good sensory characteristics. As a controlling agent of B. cereus in culture medium and in a food model of Cheonggukjang, B. subtilis SN7 efficiently inhibited growth of B. cereus vegetative cells and inactivated germination of B. cereus spores. Furthermore, B. cereus was not detected in Cheonggukjang stored at 4 °C for 6 months. B. cereus was easily detected in fermented food during storage at low temperature, as endo-spores of B. cereus are resistant to various treatments such as heat treatment and can grow even at 4–5 °C. These results suggest that bacteriocin-producing B. subtilis SN7 has great potential as a controlling agent of B. cereus and as a starter culture in Cheonggukjang.