An ideal agricultural system is economically and spiritually beneficial to both producers and consumers including human beings. It should actively preserve and protect the environment, be self-contained and regenerative, and produce enough food for an increased world population. An ideal agricultural system needs proper care on certain issues such as nutrient management, efficient utilization and recycling of energy, and preservation of natural resources and the environment. Soil microorganisms are the most abundant of all the biota in soil and are responsible for driving nutrient and organic matter cycling, soil fertility, soil restoration, plant health, and ecosystem primary production. Beneficial microorganisms include those that create symbiotic associations with plant roots (rhizobia, mycorrhizal fungi, actinomycetes, diazotrophic bacteria), promote nutrient mineralization and availability, produce plant growth hormones, Nitrogen fixation, phosphate solubilisation, potassium mobilisation, antagonism towards pathogens or diseases (biocontrol agents). Many of these organisms are already naturally present in the soil, although in some situations it may be beneficial to increase their populations by either inoculation or by applying various agricultural management techniques that enhance their abundance and activity. Farmers often think of microbes as pests that are destructive to their crops or animals (as well as themselves), but many microbes are beneficial. Soil microbes (bacteria and fungi) are essential for decomposing organic matter and recycling old plant material. Some soil bacteria and fungi form relationships with plant roots that provide important nutrients like nitrogen or phosphorus. Fungi can colonize the upper parts of plants and provide many benefits, including drought tolerance, heat tolerance, resistance to insects, and resistance to plant diseases. These beneficial microorganisms play an important role in our agriculture. Hence, the role of microorganisms in agriculture is indispensable. Since microorganisms are useful in eliminating problems associated with the use of chemical fertilizers and pesticides, they are widely been applied in natural farming and organic agriculture. Microbial biotechnology and its application in the sustainable development of agriculture and environmental health are getting better attention nowadays. The purpose of the special issue is to further prioritize the importance of microbial-based technology in the agricultural sector for the greater benefit of the scientific community as well as stakeholders.