Rhizobia, a highly specialized phyto-microbiome to fix atmospheric nitrogen, are not the only residents of legume root nodules; certain other bacteria also colonize the nodule tissues and together constitute the nodule microbiome. Culture-dependent and metagenomics approaches revealed a greater diversity of non-rhizobial components of legume root nodules which is more complex than previously thought, including bacteria from very different phylogenetic groups. Mutations in symbiotic related genes in Lotus significantly alter plant-associated bacterial community structures. Recent studies revealed the possibilities of improving soil health by cultivation of legumes through symbiosis-linked bacterial communities apart from di-nitrogen fixation. Recently, the significant contribution of nodule endophytic bacteria for the growth and survival of grain legumes and tree legumes has been established. Nodule endophytes play critical roles in the growth, development, and fitness of legumes through expressing the potential plant growth-promoting or biocontrol traits. The capacity of symbiotic rhizobia and associated non-rhizobial endophytes to produce metal scavenging compounds like siderophore can help to improve plant health under soils with sub-optimal conditions. Endophytic bacteria produce metallophores and involve in nickel uptake, transport of iron citrate, etc. Forage quality and yield of crop plants were also improved by nodule endophytic bacteria with the ability to synthesize phosphatases and auxins. Endophytic bacteria can prime the immunity of plants against phytopathogens. This chapter integrates the information about structural and functional diversity of nodule endophytic bacteria and plant health, drawing attention to exploring non-rhizobial bacteria to overcome biotic and abiotic stresses and mitigate the adverse effects caused by abiotic stresses like heavy metal stress, soil salinity, acidity/alkalinity, and drought.