Plant disease development from soil-borne pathogens involves intricate interplay between plants, soil microbiota, pathogens, and environmental factors that drive disease ecology. Advances in molecular techniques have shifted focus from individual interactions to community-based studies, uncovering how microbial dynamics influence disease progression or suppression. Meta-omics technologies encompassing metagenomics, meta-transcriptomics, meta-proteomics, and meta-metabolomics offer a comprehensive view of microbial diversity, functional roles, and interactions, providing valuable insights into disease suppression and progression. Meta-omics further elucidates mechanisms like resource competition, antimicrobial compound production, and immune modulation in disease suppression, while also identifying factors like microbial dysbiosis and pathogen synergy that intensify disease. These integrated strategies can unveil microbial diversity, gene expression, protein interactions, and metabolite pathways, providing holistic insights into plant-pathogen-microbiome dynamics. High-throughput sequencing technologies have revolutionized microbiome studies, facilitating precise characterization of microbial communities and their roles in plant health. The chapter highlights the diversity of plant microbiomes found in rhizosphere and phyllosphere, identifying core and satellite taxa that influence plant health and disease dynamics. Integrating meta-omics with ecological data is advocated to develop environment-friendly strategies for sustainable disease management and agricultural resilience.