<p>Soil and sediment metagenomics is revolutionizing our ability to understand, monitor, and enhance soil (and sediment) health—a cornerstone of climate resilience, food security, and sustainable agriculture. By decoding the genetic blueprint of soil and sediment microbial communities, and integrating artificial intelligence (AI) for real-time analysis, it enables precise interventions for nutrient cycling, bioremediation, and disease suppression. This review presents a SWOT analysis of India’s soil and sediment microbiome research, underscoring its biodiversity and scientific strengths, while identifying policy, financial, and regulatory gaps. Drawing lessons from global frameworks such as Horizon Europe, the USDA’s One Health Framework, China’s Soil Pollution Action Plan, and UN-led initiatives like the FAO’s Global Soil Partnership, it outlines strategies for India to develop a National Soil/sediment Microbiome Strategy, strengthen AI-enabled infrastructure, and reform intellectual property (IP) regimes. By linking metagenomics with digital agriculture, circular economy, and planetary health, India can position itself as a global leader in sustainable soil and sediment innovation.</p>