Different fruit crops sequestering atmospheric carbon in their perennial framework display their ability to moderate climate change-related issues on one hand and elevate the crop fertilising ability via microbes as part of green biology on the other hand. Better responsiveness of soil microbial biomass over chemically available nutrient pool to response of nutrient input, has led to renewed interest in measuring the quantum of nutrients held microbially. Long term data accrued through response of organic manuring versus inorganic fertilizers demonstrated that important soil quality indices like soil microbial diversity, soil microbial biomass nutrients (Cmic, Pmic, and Nmic) and organic carbon fractions displayed significant changes, coupled with statistically significant differences in quantum of fruit yield and fruit quality parameters. These studies led to development of microbial consortium (Paneibacillus alvei MF113275 ; Bacillus pseudomycoides MF113272 ; Micrococcus yunnanesis, MF113274 ; Acinetobacter radioresistens , MF113273 ; and Aspergillus flavus , MF113270 ) displaying encouraging results in both nurseries as well as well grown-up orchards as best management practice to cut down the rate of CO2 release compared to inorganic fertilizers for storing larger proportion of plant-derived C in long term pools in the soil and reducing the exposure of such stored C to lesser decomposition, in addition to better post-harvest shelf life of citrus and other fruits. The other approaches involving multiple microbial inoculation alongwith enrichment of organic manures through inorganic fertilizers known as substrate have further been highlighted to provide an understanding of mechanism involved in C stabilization in soils for regulating soil C sequestration and associated nutrient dynamics under INM-based production system in perennial fruit crops. We also evaluated rhizopheree hybridization approach for developing biochemically more active rhizosphere translating into elevated accumulation of nutrients and development of fruit quality. These green biology assisted fruit production system would go a long way in exploiting the role of microbes in unlocking the productivity potential.