Sustainable agriculture has soil health as one of the most critical components. Soil health is defined by Soil microorganism diversity and activity. Agricultural sustainability requires a crop production system, which can produce food without impacting the environment negatively. Healthy soil has a significant impact on the quality of food. The soil can be defined as a living system with multiple functions, including water quality and plant productivity in the ecosystem, controlling soil nutrient through recycling decomposition, and maintaining atmospheric balance by removing greenhouse gases. Beneficial microfauna such as mycorrhizal fungi species, cyanobacteria, and nematodes are part of the soil ecosystem, and they enhance water use efficiency and nutrient availability to plants, phytohormones production, soil nutrient cycling, and plant resistance to environmental stresses. One of the key challenges being faced by farmers is crop protection without the use of chemicals (technical pesticides). Studies conducted over the past 40 years on organic farms have consistently shown that disease and pest infestations are significantly lower compared to chemical farms. Nitrates from fertilizers like urea and ammonium (such as DAP) act as a magnet, attracting insects and pathogens from the insect world, as they require these compounds for their own protein synthesis. This supports the observed mechanism that the greater the use of chemical fertilizers, the higher the vulnerability of crops to diseases and pest attacks. Farming practices have shown that organic farming and conservation tillage improve soil health by increasing the abundance, diversity, and activity of microorganisms. Conservation tillage can also potentially increase the grower’s profitability by reducing inputs and labor costs as compared to conventional tillage. In this chapter, we will emphasize the challenges in today’s agriculture and the need for time to take suitable steps by harnessing modern techniques to improve rhizosphere microbiota and the impact of crop management practices on soil health for sustainable crop production.