The improvement of the effectiveness and survival of rhizobia in the rhizosphere of legume host plants is a common practice in agricultural legume production. We have recently reported that the overexpression of IAA in S. meliloti 1021 played a positive role in the adaptation to various stress conditions both in free-living bacteria and in nodulated plants. We show here that IAA triggers the coordinate enhancement of various cellular defense systems and that IAA-treated bacteria are more resistant to desiccation. In addition, Medicago plants nodulated by the IAA-overproducing strain RD64 (Mt-RD64), restore auxin/cytokinin balance by increasing the transcription of cytokinin signaling genes. Finally, we bring here that RD64 is less competitive in comparison to the wild type strain under normal conditions, but it works better under salt stress conditions.