Dietary supplementation with lactic acid bacteria to maintain or improve intestinal health is advocated. Weissella spp. are present in different fermented vegetable‐based foods like kimchi , as well as in the normal gastrointestinal (GI) tract of humans. Weissella cibaria strains have been proposed as potential probiotics. Freeze‐drying is a promising treatment method for these strains for industrial applications and to increase the accessibility of their health‐promoting benefits. Moreover, probiotic strains need to be able to survive in the host GI tract, and acid and bile are both environmental stressors that can reduce strain survival. Therefore, this study evaluated the effect of the combination of protective agents on the acid and bile resistance of W. cibaria JW15 after freeze‐drying. A protective agent combination with a 1:1 ratio of 5 g + 5 g/100 ml w/v soy flour + yeast extract (SFY) retained nearly 100% viability after freeze‐drying and was resistant to artificial bile acids. Remarkably, skim milk + soy flour (SSF) was resistant to an acidic solution, and the viability of W. cibaria JW15 in artificial gastric acid was enhanced when treated with this mixture. Furthermore, SFY and SSF were found to maintain high numbers of viable cells with a low specific rate of cell death ( k ) after storage at 50°C, 60°C, and 70°C. These results support an effective probiotic formulation system with a high number of viable cells, and its protective effects can be leveraged in the development of probiotic products with health benefits.