Healthy soils are fundamental to sustainable food systems and are at the heart of global challenges around food security, climate change adaptation, biodiversity conservation and environmental health. Yet, an estimated 60-70% of EU soils are currently classified as degraded, prompting policy action to protect soils. Soil microbial communities underpin many of the ecosystem services provided by soils — driving nutrient and carbon cycling, enhancing plant productivity, suppressing pathogens and increasing system resilience — yet they remain the least understood component of soil health. The abundance, diversity and functioning of soil microorganisms are strongly impacted by agricultural practice, so managing our soils in a manner that safeguards microbial function is essential for sustainable food production. Recent molecular and computational advances have transformed our capacity to characterise soil microbiomes and link community composition to function, opening up opportunities to steer microbial communities towards improved agronomic and environmental outcomes. However, examples of successful translation into practical, evidence-based farm-level application remain limited. Methodological challenges specific to the soil environment also hamper implementation of certain microbial tools, limiting insights. Here, recent progress in soil microbiome research is synthesised. The potential and barriers to harnessing microbiome knowledge to inform agricultural management are discussed, and how microbial diversity relates to soil multifunctionality is examined. The effectiveness of soil microbial analysis as an indicator of the national soil resource is evaluated as well as the potential impact of climatic stress on soil microbial communities.