Salinity is a major abiotic stress for crop plants that cause reduced food production. The application of plant growth-promoting microorganisms can improve the adaptability of plants to biotic and abiotic stresses. Therefore, in the current study, we aimed to enhance the mitigation effects of artificially applied rhizobacterium Klebsiella variicola AY13 on salinity stress in Trifolium repens L. The results suggested that AY13 innately produced indole-3-acetic acid and accelerated the morphological adaptation of T. repens to salt stress conditions. Furthermore, AY13 promotes a Trp-dependent pathway for indole-3-acetic acid (IAA) production, as adding L-tryptophan (L-Trp) increased IAA production in pure culture. AY13 improved plant growth by maintaining relative water content and minimizing water loss in excised leaves. Moreover, AY13 inoculation significantly reduced the endogenous levels of abscisic acid and antioxidants such as glutathione and catalase. These results suggest that AY13 plays a crucial role in reprogramming stress-related metabolism and enhancing plant stress tolerance.