Abiotic stresses like drought, high temperature, salinity, and alkalinity are major constraints in the agricultural production system. Crop plants adapt to external pressures imposed by environmental and soil conditions through intrinsic biological mechanisms. Failure to do so results in compromised growth, development, and yield. Consequently, gaining a deeper understanding of the stress-mitigating mechanisms in crops is vital for enhancing productivity. Meta-omics approaches, i.e., encompassing genomics, transcriptomics, proteomics, metabolomics, and phenomics, allow researchers to study plant–microbe interactions comprehensively. These advanced tools provide valuable insights into the complex defense mechanism of microbes, opening new possibilities for boosting plant resistance to abiotic stresses. This chapter aims to explore how omics technologies are transforming our understanding of plant gene regulation for the defense system in legumes, which are critical for advancing sustainable agricultural practices. Furthermore, the meta-omics techniques within a unified framework can enhance our ability to address these challenges and understand to deepen our knowledge of plant meta-omics, facilitate the development of effective solutions, and ultimately contribute to global food security in the face of climate change and environmental stressors.