One of the challenges in the practical application of plant growth-promoting bacteria (PGPB) is predicting their effectiveness under field conditions. Performance can vary due to environmental factors and the recruitment of genotype-specific microbiota through root exudates. In addition, the viability of PGPB during storage and delivery must be maintained to avoid inconsistent field performance. Lyophilization (freeze-drying) is a promising method for preserving bacterial cells; however, this process subjects bacterial cells to extreme thermal and osmotic stresses that can lead to irreversible cellular damage. In this study, the addition of crude soybean seed extract, with 10% glycine betaine and 5% cellobiose as cryoprotective agents, improved bacterial viability after freeze-drying with high recovery rates of 82–98% after preservation, which is essential to ensure the efficacy of beneficial soil bacteria used as biotic agents. To our knowledge, this is the first study to report optimal preservation conditions for beneficial soil bacteria shown to promote soybean growth, providing a basis for improving soybean yield through microbial applications.