The history of microbiological research in various geological sciences is analyzed in brief. Development of the doctrine about underground microorganisms and its use in various engineering geological schools is shown on the basis of experimental studies, including modern metagenomic analysis. The primary sources of the microorganisms’ penetration into the underground space of St. Petersburg have been identified and systematized according to different principles. The analysis of engineering geological processes as a result of microorganisms and products of their vital activity provides the main aspects that control safety of subsurface exploration and use for various purposes, including the design, construction and operation of underground structures (subway tunnels) at different depths, as well as running deep foundation pits for ground structures. The results of experimental studies of the subsurface microorganisms’ activity make it possible to infer that it is necessary to extend engineering geological, hydrogeological and engineering ecological research of the urban underground space in order to assess the hazard of the underground microorganisms’ activity and to mitigate emergency cases for engineering structures.