Symbiotic and associative interactions with beneficial microorganisms (MO) are the keystone of plant performance. The plant microbiome plays crucial roles in plant life such as nutrient fortification, defense against pathogens and pests and mediating of multiple abiotic stresses. This chapter focuses on the microbiome's role in plant nutrition facilitation. The plant-associated MO inhabiting the mycorrhizosphere and rhizosphere are the most promising group for agricultural application. Their numbers increase in the root zone, and there microbial-driven chemical transformation and nutrient mobilization are more prominent than in bulk soil. Root-associated MO are of particular importance in various compounds’ chemical transformation, are able to change the soil structure by both physical and chemical mechanisms, and to provide defense against deleterious organisms and stresses. Thus, the underground microbiome contributes largely to the plant performance and requires much attention from the position of sustainable agriculture.