The maintenance of intracellular nitrogen-fixing bacteria causes changes in proteins' location and in gene expression that may be detrimental to the host cell fitness. We hypothesized that the nodule's high vulnerability toward salt stress might be due to alterations in mechanisms involved in the exclusion of Na from the host cytoplasm. Confocal and electron microscopy immunolocalization analyses of Na/K exchangers in the root nodule showed the plasma membrane (MtNHX7) and endosome/tonoplast (MtNHX6) signal in non-infected cells; however, in mature infected cells the proteins were depleted from their target membranes and expelled to vacuoles. This mistargeting suggests partial loss of the exchanger's functionality in these cells. In the mature part of the nodule 7 of the 20 genes encoding ion transporters, channels, and Na/K exchangers were either not expressed or substantially downregulated. In nodules from plants subjected to salt treatments, low temperature-scanning electron microscopy and X-ray microanalysis revealed the accumulation of 5-6 times more Na per infected cell versus non-infected one. Hence, the infected cells' inability to withstand the salt may be the integral result of preexisting defects in the localization of proteins involved in Na exclusion and the reduced expression of key genes of ion homeostasis, resulting in premature senescence and termination of symbiosis.