Food security is under unprecedented threat due to factors such as rapid population growth, climate change, and significant postharvest food losses. The plant microbiome, a complex community of microorganisms associated with plants, holds significant potential for enhancing agricultural sustainability and ensuring food security. This chapter provides a comprehensive review of omics technologies—genomics, transcriptomics, proteomics, metabolomics, and metagenomics—as tools for understanding plant–microbiome interactions and their role in improving plant resilience to abiotic stresses, including drought, salinity, and heat. By integrating omics data, we can decode the intricate relationships between plants and their associated microbes, revealing mechanisms by which beneficial microbes enhance plant stress tolerance. We discuss nondestructive methods like phenomics and imaging, which offer valuable insights into plant responses under various stress conditions without compromising plant integrity. Additionally, the chapter highlights the transformative potential of web-based omics platforms and artificial intelligence in advancing microbiome research, facilitating the development of predictive models for stress tolerance, and guiding crop improvement strategies. The application of these advanced technologies promises to drive innovative solutions for sustainable agriculture. However, significant challenges remain, including data integration, scalability, and translating omics insights into practical agricultural practices.