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Rhizobium strains play a crucial role in sustainable agriculture by enhancing plant growth and stress tolerance. In this study, twelve bacterial isolates were obtained from root nodules of Vigna radiata and Cajanus cajan, with 10 confirmed as Rhizobium spp. through 16S rRNA sequencing. Isolate RZ5 showed the highest IAA production (38.6 ± 1.2 µg/mL), phosphate solubilization (2.1 ± 0.1 cm halo), and ACC deaminase activity (28.4 ± 1.1 nmol α-ketobutyrate/mg protein/h). Greenhouse experiments revealed that Rhizobium inoculation significantly improved plant performance under drought and salinity stress. Inoculated plants under drought exhibited a shoot length of 16.5 ± 1.1 cm and fresh biomass of 5.5 ± 0.4 g, compared to 12.7 ± 0.9 cm and 3.8 ± 0.3 g in uninoculated controls. Under salinity stress, inoculated plants had a shoot length of 17.1 ± 1.2 cm and fresh biomass of 5.8 ± 0.5 g, outperforming controls (13.2 ± 1.0 cm and 4.0 ± 0.4 g). Physiologically, inoculated plants maintained higher chlorophyll content (39.5 ± 2.1 SPAD units under drought; 42.1 ± 2.2 under salinity) and relative water content (78.4 ± 2.0% and 80.2 ± 2.1%), while exhibiting lower electrolyte leakage. Moreover, soil nutrient properties improved, with inoculated drought-stressed soils showing increased total nitrogen (0.16 ± 0.01%) and available phosphorus (10.5 ± 0.7 mg/kg). These findings highlight the potential of Rhizobium-based biofertilizers to enhance plant resilience and soil health under adverse environmental conditions, supporting sustainable agriculture practices.