Soil is of vital importance in the production of crops, although it is sometimes disregarded or solely considered as a physical support for plant growth. But given the growing public concerns about agriculture's sustainability, soil has to be seen as a living system. The biological, chemical, and physical characteristics of soil that are necessary for long-term, sustainable agricultural productivity with little negative influence on the environment are referred to as soil health. As a result, soil health offers a comprehensive view of soil functionality. This has led to a resurgence of interest in traditional methods like applying organic amendments. These methods have a significant impact on soil health, which considers plant health, by altering the physicochemical properties of the soil as well as its microbial populations. Furthermore, the important participants in each agro-ecosystem are microorganisms. They are the native residents of every soil and plant system, and because of their wide range of functional capacities and multifaceted existence, they constitute dominating presence in these systems. As a result, microbes and microbial methods are widely employed as measurement of soil health because to their well-established contribution to many aspects of soil health. A variety of microbe-based metrics are commonly used worldwide. We offer suggestions on how to better direct and enhance the use of microbiological data to produce pertinent and useful evaluations of soil health and, eventually plant health.