Innovative strategies transcending conventional breeding and genetic modification approaches are the need of the hour for sustainable and resilient agriculture systems. In recent years, among the most transformative advances are meta-omics technologies comprising metagenomics, metatranscriptomics, metaproteomics, and metabolomics that collectively enable a systems-level exploration of plants and their associated microbiomes. These are powerful tools to decipher intricate and complex relationship within plant microbiomes and their effect on plant health and productivity that are instrumental in enhancing crop productivity. These also provide unprecedented insights for understanding plant–microbiome interactions by identifying microbial communities’ structure and dynamics under diverse environmental conditions. By integrating diverse layers of molecular information, hidden mechanisms of effective use of nutrient and resilience to stress and disease are being unrevealed by researchers. These insights are important and can provide a foundation for next-generation crop improvement strategies for soil fertility enhancement, improving resilience against various stresses in crops and bioremediation, thereby promoting overall crop improvement, environmental sustainability, and restoration of the ecosystem.