<p>Health of soil has a vital role in sustainable agriculture to ensure food security and preserve the environment. Global food demand is rising day by day, and crop plants fall in front of many challenges due to degeneration of soil as a result of non-judicious application of chemicals as well as water and air pollution. Collaborative efforts by farmers, policymakers, and researchers to promote sustainable practices are today’s need. Strategies like cover cropping, crop rotation, reduced tillage, organic matter addition, integrated nutrient, and pest management are required for betterment of soil health and securing long-term agricultural viability. Management options for improving soil health are also necessary to mitigate different biotic and abiotic stresses and enhance crop yield. Stressors to soil biodiversity include excessive grazing, declining soil organic matter, pollution, soil erosion, land degradation, intense human usage, climate change, and loss of aboveground biodiversity. Assessment of the threats to soil biodiversity and taking appropriate action are required for sustainability of agriculture in world. Microbial capacities are generally linked to soil health and sustainability of agriculture through their functional abilities to nutrient acquisition, mobilization, fixation, recycling, decomposition, degradation, and remediation in soil. This review deals with important variables to take into account when evaluating the soil biodiversity, soil quality, and principles as well as components of soil health in sustainable agricultural systems.</p>