Healthy soils are an invaluable resource for sustainable agriculture and soybean farming communities. Intensive agriculture accompanying with reduced crop diversity, tillage and excessive chemical fertilizers can have deleterious effects on soil health. In recent years, the degradation of agricultural soils due to erosion, compaction and pesticide contamination has highlighted the urgent need of caring for soil’s capacity to sustain agricultural production and maintain essential soil functioning. Consequently, ‘soil health’ has garnered considerable attention in the last two decades. There is a growing awareness among soybean producers about the significance of soil health and the practices that can maintain healthy soils. While the physical and chemical indicators of soil health have been emphasized, the biological indicators have received little recognition. Considering the role of microbes in soil ecosystem services, microbial indices must be integrated in soil health practices. Furthermore, the current perception of microbial contribution to soil health is simplistic and reductionist as it only considers indices such as the overall microbial biomass, fungi: bacteria or soil enzymes. Such microbial indices can also be context-dependent. For example, higher biomass and of fungal abundance may also include greater plant pathogens or microbes that do not promote crop growth. This points to a need of integrating more relevant microbial matrices that can strengthen the concept of soil health and enable producers to implement tailored management practices. Microbiome research has achieved incredible heights in the last decade wherein latest molecular techniques have revealed unprecedented details of microbial characteristics. Soil health index must therefore integrate next-generation microbial indices. The proposed study will fill this informational void by including measurements such as microbial community composition, microbiome complexity, abundance of crop-growth-promoting microbes, protists, and other functional groups. More importantly, we will inform soybean growers about the role microbiomes in soil health.