Spore-forming, plant growth-promoting bacteria (PGPR) offer extraordinary opportunities for increasing plant productivity in climate change scenarios. Plant–water relationships, root development and photosynthetic performances are all key aspects of plant physiology determining yield, and the ability of PGPR to influence these in a coordinated manner is crucial for their success. In this study, we dissected the mode of action of a commercial Bacillus paralicheniformis FMCH001 in promoting soybean (Glycine max, seed variety: Sculptor) establishment in well-watered and drought conditions. We found that FMCH001 colonizes the roots, improved root growth and allowed plants to absorb more nutrients from the soil. FMCH001 inoculation had no effect on abscisic acid in leaf or xylem sap, while significantly improved photosynthesis rate, stomatal conductance and transpiration rate at 28 days after planting when drought stress exposed for 7 days, with depressed leaf water potential and osmotic potential. Moreover, the bacterium increased water use efficiency and the inoculated soybean plants exposed to drought used 22.94% less water as compared to control, despite producing comparable biomass. We propose that the ability of the bacterium to promote root growth and also modulate plant water relations are key mechanisms that allow FMCH001 to promote growth and survival in dicotyledon plants.