The formation of new soil and nutrient availability became a recent approach in sustainable agriculture. Neoformation consist of various process such as addition of organic matter, microbial activity, symbiotic interaction, and Nutrient Cycling. These processes are the important part in the formation nutrients into of soil. For this purpose, microbiome play important role in maintenance of soil health. Microbiomes are the collection of microorganisms found in the soil environment. These helpful microorganisms engage in a variety of plant growth-promoting activities, like fixing, mineralizing, solubilizing, and mobilizing nutrients, producing siderophores, antagonistic substances, antibiotics, and releasing substances that stimulate plant growth, like auxin and gibberellin hormones, through interactions with the roots of the host plant. Some species of plant make symbiotic associations with microbes and profit from the availability of minerals and nutrients while using little energy. The distribution of plant species determines the nature and amount of root exudates, as well as the crop species and cultivars. On the other side, it is possible to isolate, formulate, and create biofertilizers from microbes that play crucial functions in the microbiome. In agriculture, significant microorganisms with Fe- and Zn-solubilizing properties can be employed to biofortify micronutrients in various cereal crops. A safe environment is achieved through sustainable agriculture, which in turn has a good impact on soil health when it is used effectively. The subject of future research will be how to promote crop growth by shaping soil characteristics with the help of plant microbial communities and organic amendments in the soil. This chapter illustrates how microbiomes help in the neoforming of crops and the integration of nutrient into the soil.