Worldwide agriculture is facing an enormous challenge that requires rapid action and sustainable technology. Application of bacteria from the endogenous microbiome encompasses a very promising option to reinforce plant resilience and productivity, due to a number of traits that may lead to beneficial symbioses. Contemporary research aims to understand the molecular mechanisms underlying rhizobacteria-mediated plant growth promotion, and therefore, opens the way for crop improvement. However, no single bacterial trait really determines plant biomass accumulation, but it might be the combination of a number of factors such as the recognition of small-secreted bioactive molecules (i.e. auxins, cyclodipeptides, and N-acyl-L-homoserine lactones) that acting in concert could modulate root architecture, nutrient acquisition and plant defense. In addition, nutrient solubilization and activation of the molecular mechanisms for nutrient acquisition may not only enhance productivity in fertile soils, but also in challenging soils, such as alkaline soils from desert and salty areas. Altogether, the chemical and nutritional mutualisms lead to highly dynamic plant and bacterial behaviors that may change with time and upon availability of resources, and thus deciphering such complex interplay is required to identify promising isolates for the formulation of inoculants. The aim of this chapter is to summarize and integrate recent data into how plant growth promoting rhizobacteria enhance plant resilience via three main mechanisms, namely chemical plant-bacteria communication, nutritional reinforcement and adaptation to challenging soils.