A model for regulating the viability and efficiency of nodule bacteria to increase soybean productivity has been developed. The component of this model is a block that assumes the use of a complex of chemical compounds (CCS). The complex consists of polymers and compounds of protein nature (sodium alginate, starch, gelatine), which, in addition to protective action, contribute to better fixation of rhizobia on seeds. In the field experiment conditions it was established that the greatest effect of soybean bacterization can be obtained by strain of nodule bacteria Bradyrhizobium japonicum and complex of chemical substances. The developed model has demonstrated its viability. In compared without CCS the combined use of microbial inoculum and CCS contributed the formation of balanced symbiotic system, increase the level of molecular nitrogen fixation. In a field experiment inoculation of soybean seeds with B. japonicum and CCS to increase the level of soybean yields by 12–13% compared to the inoculation without CCS. The effectiveness of the combination of CCS and B. japonicum in the processing on the day of sowing and one month before sowing of seeds was studied. It has been shown that the effectiveness of treatment with B. japonicum and CCS in advance was less efficient in terms of yield formation relatively same variant of treatment of seeds directly pre-sowing.