The soil microbiome in particular is essential for preserving plant health and biomass production. The management of soil microbial communities, whether targeted or inadvertently, appears to have potential for improving food crop yield, quality, and sustainability in the long run. With the development of innovative nano-tools for quick disease diagnosis and improved plant nutrient uptake, nanotechnology holds promise for advancing the agricultural and food industries. Utilizing nano-materials in agriculture offers a special chance to maintain soil health and increase crop yield. The use of nanotechnology in agriculture holds great promise for specific applications such as the development of nano-pesticides and fertilizers that can boost productivity without contaminating soils and offer protection against microbial diseases and insect pests. This chapter provides the current updates along with the sustainability issues, climate change food security and also the future prospects of nanotechnology in soil health management and crop production.