The next generation technologies have enabled in-depth investigation of plant root-microbe interactions through various omics approaches, such as genomics, metagenomics, transcriptomics, translatomics, proteomics, and metabolomics. These omics technologies decipher gene functions and its structures, reveal insights into the microbial diversity, transcript differences and its differential expressions, provide ideas for protein-protein interaction networks, and several models for metabolic processes and network. Collectively, these techniques enhance our understanding of the role of omics in plant root-microbe interactions. This chapter provides a comprehensive overview of different omics approach in elucidating beneficial role of plant-microbe interactions, which helps to the development of sustainable agricultural practices.