Extension of the storage stability of freeze-dried lactic acid bacteria is important for industrialization. In this study, the effect of cation influx from soy powder, which contains high amounts of cations, as a cryoprotective agent on the viability of freeze-dried Lactobacillus brevis WiKim0069 was tested. Compared to that in the absence of the soy powder, bacterial viability was significantly higher in the presence of soy powder. Approximately 4.7% of L. brevis WiKim0069 survived in the absence of the protective agent, whereas 92.8% viability was observed in the presence of soy powder. However, when cations were removed from the soy powder by using ethylenediaminetetraacetic acid (EDTA) and a cationic resin filter, the viability of L. brevis WiKim0069 decreased to 22.9–24.7%. When the soy powder was treated with ethylene glycol tetraacetic acid, the viability was higher than when it was pretreated with EDTA and a cationic resin filter, suggesting that Mg2+ had a role in enhancing the viability of L. brevis WiKim0069. Cold adaptation at 10 °C prior to freeze-drying had a positive effect on the storage stability of freeze-dried L. brevis WiKim0069, with 60.6% viability after 56 days of storage. A decrease in the fluorescence polarization value indicated an increase in membrane fluidity, which regulates the activity of ion channels present in the cell membrane. Cold adaptation caused activation of the cation channels, resulting in increased intracellular influx of cations, i.e., Ca2+ and Mg2+. These results suggest that cold adaptation can be used to improve the storage stability of L. brevis WiKim0069.