When subjected to nutritional stress, bacteria modify their amino acid metabolism and cell division activities by means of the stringent response, which is controlled by the Rsh protein in alphaproteobacteria. Although nutritional stress is common for rhizobia while infecting legume roots, the stringent response was scarcely studied in this group of soil bacteria. In this report, we obtained a mutant in the rsh gene of Bradyrhizobium diazoefficiens, the N2-fixing symbiont of soybean. This mutant was defective for type-3-secretion system induction, plant-defense suppression at early root infection, and competition for nodulation. Furthermore, the mutant produced smaller nodules, although with normal morphology, which lead to lower plant biomass production. The autoregulation of nodulation in N-free condition was compromised in plants inoculated with the mutant, but it nodulated plants in the presence of 10 mM NH4NO3, a combined-N concentration inhibiting nodulation. The rsh mutant released more auxin to the culture supernatant than the wild-type, which might in part explain its symbiotic behavior in the presence of combined-N. These results indicate that B. diazoefficiens stringent response integrates into the plant defense suppression and autoregulation of nodulation circuits in soybean, perhaps mediated by the type-3-secretion system.