Plant growth-promoting rhizobacteria (PGPR) are integral components of soil and rhizosphere microbiomes, contributing to plant growth, nutrient acquisition, and tolerance to biotic and abiotic stresses. Although research has largely focused on PGPR inoculants, most PGPR in agroecosystems are indigenous soil communities. Harnessing and enhancing these indigenous populations is central to sustainable agriculture yet remains less developed than strain-based bioproduct approaches. This chapter synthesises current knowledge on the ecology, assembly, and functioning of indigenous PGPR and evaluates management strategies to promote their in-situ persistence. We examine drivers of PGPR community structure, including soil properties, plant genotype, root exudation, land use, and agricultural inputs, and characterise them using both culture-dependent and culture-independent methods. Agronomic practices that steer microbiomes towards beneficial states are assessed, while a critical discussion addresses context dependence, inconsistent field responses, ecological risks, and key knowledge gaps linking PGPR community shifts to agronomic outcomes and informing soil health frameworks and resilient cropping systems.