Aims: The purpose of this research was to compare root exudation of major organic components, effects of PGPR on root exudates and the response of different soybean varieties to inoculation with PGPR to understand variety-dependent relationships between these traits. Methods: Growth and root exudation of soybean varieties Nice-Mecha, Bara and Svapa in the absence and presence of PGPR Pseudomonas oryzihabitans Ep4 was studied using gnotobiotic hydroponic system and UPLC techniques. Rhizobacterial effects on growth, seed yield quality, nodulation by Bradyrhizobium japonicum 634b and uptake of nutrients was investigated under field conditions. Results: Genotypic differences between soybean varieties in root exudation, rhizobacterial effects on exudation and interactions with Ps. oryzihabitans Ep4 were revealed. Variety Bara had greatest root biomass with least root exudation and least Ps. oryzihabitans Ep4 colonisation. In both hydroponic experiments and field trials, the varieties Nice-Mecha and particularly Svapa responded more actively to Ps. oryzihabitans Ep4 than the variety Bara. Several mechanisms related to root exudation rate, exudate composition, bacterial production of siderophores and auxins are proposed to explain variety dependent interactions of plants with PGPR. Conclusions: The variety specific plant response to PGPR is mediated by genotypic differences in root exudation and the ability of PGPR to metabolize and/or transform the exuded organic acids, sugars and amino acids.