The beneficial microbes plays an important role in medical, industrial, and agricultural processes. The precious microbes belong to different groups including archaea, bacteria, and fungi which can be sort out from different habitat such as extreme environments (acidic, alkaline, drought, pressure, salinity, and temperatures) and associated with plants (epiphytic, endophytic, and rhizospheric) and human. The beneficial microbes exhibited multifunctional plant growth promoting (PGP) attributes such as N 2 -fixation, solubilization of micronutrients (phosphorus, potassium and zinc), and production of siderophores, antagonistic substances, antibiotic, auxin, and gibberellins. These microbes could be applied as biofertilizers for native as well as crops growing at diverse extreme habitat. Microbes with PGP attributes of N 2 -fixation, P-, and K-solubilization could be used at a place of NPK chemical fertilizers. Agriculturally, important microbes with Fe-and Zn-solubilizing attributes can be used for biofortification of micronutrients in different cereal crops. The biofertilizers are an eco-friendly technology and bioresources for sustainable agriculture and human health. In general, the concentrations of micronutrient in different crops are not adequate for human nutrition in diets. Hence, consumption of such cereal-based diet may result in micronutrient malnutrition and related severe health complications. The biofortification approach is getting much attention to increase the availability of micronutrients, especially Fe and Zn in the major food crops. The beneficial microbes can be used as probiotic as functional foods for human health. Probiotics microbes such as Bifidobacterium, Lactobacillus, Methanobrevibacter, Methanosphaera, and Saccharomyces are increasingly being used as dietary supplements in functional food products. The microbes with beneficial properties could be utilized for sustainable agriculture and human health.