The formation of new soil and nutrient availability became a recent approach in sustainable agriculture. Neoformation consists of various processes such as the addition of organic matter, microbial activity, symbiotic interaction, and nutrient cycling. These processes are the important part in the formation of nutrients in soil. For this purpose, microbiomes play an important role in the 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, and 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 nutrients into the soil.