Cowpea is a major grain legume crop mostly grown in sub–Saharan Africa, Asia, and South America. Drought and nutrient deficiency affect the growth and yield of cowpea. To address this challenge, we studied the phytobeneficial effects of stress tolerant rhizobacteria on the biomass yield of cowpea under water and nutrient deficit conditions. Among the bacteria isolated, two rhizobacillus genotypes, Bacillus filamentosus (C8) and Bacillus aryabhattai (C29) were evaluated for the improvement of seed germination and growth of cowpea under stress. Our study revealed that C8 protected cowpea from stress by facilitating phosphorus and potassium uptake, protecting from oxidative damage, reducing transpiration and enhancing CO2 assimilation. A 17% increase in root biomass upon C8 inoculation was concomitant with the induction of stress tolerance genes in cowpea root that are predominantly involved in growth and metabolic processes, cell wall organization, ion homeostasis and cellular responses to phosphate starvation. Our results indicate metabolic reprogramming in cowpea root triggered by B. filamentosus, leading to efficient nutrient reallocation in the host plant. We propose inoculation with B. filamentosus as an effective strategy for improving yield of cowpea in low-input agriculture, where chemical fertilization and irrigation are less accessible to resource-poor farmers.