Soil health fundamentally reflects biological processes in the soil ecosystem. The development of soil health frameworks and associated indicators have increasingly prioritized biologically relevant characteristics of soil. Some of these properties, like soil organic carbon, reflect resources available for microbes. Others, like community composition, indicate the functional potential of the microbiome to participate in soil processes. The synergistic effect of resources and functional potential are manifested in indicators, such as carbon mineralization, that measure microbial activity. To better interrogate the variable states of soil health, underlying influences on biological indicators should inform both selection of indicators to study and interpretation of results. In this chapter we discuss the historical methodology that eventually led to soil health research, current efforts to refine biological indicators, and more advanced techniques that might eventually be integrated into soil health frameworks.