Sustainable agriculture is a system of farming using a microbe that protects the environment, maintains natural resources, produces healthy foods, and minimizes the use of chemical pesticides or fertilizers. Soil microbes like bacteria and fungi play an essential role in maintaining soil fertility, decomposing organic matter, and recycling nutrients. The presence of microorganisms in soil depends on the soil properties like moisture, pH, temperature, oxygen, salinity, porosity. Rhizosphere microbial communities play important role in plant protection, growth promotion, and production of antibiotics. Soil horizon maintenance is also vital for soil health and quality. The soil environment consists of a variety of physical, chemical, and biological factors that directly affect the diversity of microbes. For sustainable agriculture, soil-microbial diversity is important for ensuring soil productivity, and increase in crop production. The microbial technologies, for instance, gene-editing system, RNAi mediated gene silencing, proteomics, Genetic engineering, Metagenomics, Metatranscriptomics, and microbial whole-genome sequencing are used for sustainable agriculture. In this review, we investigated magnitude of microbes in sustainable agricultural development.