The preservation of natural ecosystems, as well as the correct management of human societies, largely depends on the maintenance of critical microbial functions associated with soils. Soils are biodiversity rich pools, and rhizosphere soils can be associated with increased plant functions in addition to the regulation of nutrient cycling, litter decomposition, soil fertility and food production by agriculture systems. The application of biocontrol agents or plant growth-promoting bacteria has been tested in order to colonize roots at initial stages and offer advantages by promoting healthier and higher-yielding crops. In this review we describe the efforts to develop more sustainable systems that seek to minimize environmental disruption while maintaining plant health. Particular emphasis is given in this review to soil improvement strategies and the taxonomic groups involved in plant growth and protection against biotic stresses. It is important to define the impacts of land management and crop production practices on the structure and composition of soil bacterial communities. By promoting, monitoring and controlling the plant microbiome, and understanding the role of certain biocontrol agents within the plant throughout the lifecycle of the plant, we may substantially improve nutritional and environmental standards and reduce the negative impact of some agrochemicals. The integration of biological alternatives with traditional strategies may be critical to improve the sustainability of agriculture systems.