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Maintenance of soil health is central to agricultural sustainability and a key factor that reflects the productivity of agro ecosystems. However, at present the soil resources are under severe threats from various anthropogenic activities including climate change. Climate changes add more uncertainties and complexities to agriculture, ecosystem and intimidate their sustainability. Plant-associated microbial communities stimulate the plant growth and increase their resistance to various abiotic and biotic stresses. Linking the distribution of microbial diversity and ecosystem functioning is essential to understand ecosystem responses to changing environment. Soil microbial taxa are imperative in relation to global climate changes as they play important and undisputable roles in biogeochemical cycling, plant growth and carbon sequestration. Modern genomic approaches show tremendous potential for identification of uncultivated diversity and finding shifts in the bacterial community associated with sensitive and disease tolerant plants, and understanding how microbes are affected by climate change. In this review, we discussed how the climate change influences soil microbial communities and plant-microbe interactions. Further, in this review the we have highlighted the role of metagenomics for unlocking the soil microbial black box.