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Climate-smart agriculture is a multidisciplinary farm model approach that helps reduce the impact of climate change not only on soil but on entire agricultural systems. One of the critical approaches of climate-smart agriculture is using the soil microbiome to help the crop adapt to the changing climate and increase crop production. The microorganisms that are present in the soil play a crucial role in ecosystem services, crop protection and performance, and productivity. Legumes are essential for their nutritional value and interaction with soil microbes, particularly in fixing atmospheric nitrogen and improving soil health through plant-microbe association. Beyond Rhizobium, a wide range of microorganisms and fungi assist legumes in adapting to climate stresses such as drought stress and salinity, which ultimately enhances biomass and legume yield. However, the molecular mechanisms behind the interactions between microbiomes and plant growth, ecosystem services, and carbon sequestration remain unclear in legumes. This review aims to explain the key roles of the soil microbiome, legume rhizobiome, and the microbial genes associated with functional plant traits that help plants adapt to a changing climate. Understanding how microbial populations shift due to climate variations and how these changes affect legume yields is crucial, given the ever-changing nature of ecosystems due to climatic shifts. Therefore, more research is warranted to explore plant microbial interactions, understand the dynamics of climatic shifts, and develop microbiome engineering tools for the improved health of crop and rhizobiome ecosystems. Furthermore, a parallel study is required to examine the harmful microbiome that causes crop destruction and antagonizes important bacteria.