The review summarizes the most relevant microbiological characteristics that can serve as indicators of soil ecological functions: bioresource, phytosanitary, as well as the functions of carbon transformation and plant nutrition. The indices of diversity and taxonomic structure of microbial communities as well as abundance of certain groups of microorganisms are estimated to characterize the bioresource function of soils. The main microbiological indicators of carbon transformation are microbial biomass carbon, the ratio of bacterial to fungal biomasses, soil respiration, enzyme activities, and the rate of soil organic matter decomposition. The appropriate microbiological indicators of the plant nutrition function of soil are the enzyme activities associated with the nitrogen and phosphorus cycles, as well as molecular species-specific markers of arbuscular mycorrhiza. Gene abundances of phytopathogens and their antagonists can serve as indicators of soil phytosanitary function. Since a high variation of some characteristics and certain difficulties in their interpretation are currently the relevant problems in microbiological indication of soil functions, the key goal is a careful selection of the parameters with the best applicability as indicators of soil ecological functions.