Maintaining healthy soils are necessary for developing healthy ecosystems and sustainable agricultural production. It is widely accepted that soil health is a very important management tool to correct unproductive and illness of soil. There is still a lack of clarity about how to measure soil health or what indicators should be taking care of for a satisfying conclusion, considering soil health is not wholly output of soil physical and chemical properties but includes soil biological characteristics. Biological activities mostly occurred in topsoil range up to 30–45 cm soil depth, where most of the soil microbes are living, comprising a tiny portion of about 0.5% of total soil volume and nearly 10% of total soil organic matter. Despite their small population, microbes play a vital role in organic matter decomposition and nitrogen-phosphorus-sulfur cycling. This way soil microbes transformed organic residues into readily available nutrients to plants. They also lead to the degradation/decomposition process of waste materials and some synthetic compounds. Soil microbes produce polysaccharides, which act as soil cementing agent and help in maintaining soil structure, improving aeration and water holding capacity, reducing soil crusting and compaction. Soil microbe shows the capability to assess the integrated measure of soil health, which cannot be achieved through chemical or physical assessment. They respond very quickly to surrounding environmental changes as well as environmental stress conditions. Thus, soil microbes can be an outstanding indicator of soil health. Therefore, there is a need to study on identification, dynamics, and efficiency of soil microbes capable to indicate soil nutrient status or stress conditions, for early signs of soil health improvement or alert to soil degradation. This chapter extensively focuses on the role of soil microbes to indicate soil health status.