In the face of today’s climate change challenges, the first few kilometers of the Earth’s crust are being scrutinized with increasing covetousness, as the resources or interstitial space they offer will be one of the keys to our future energy strategies (as for example geothermal or gas storage–i.e., town gas, anthropogenic CO2, and in the near future H2–or even a combination of these). Although our knowledge of subsurface ecosystems has progressed in recent years, it is not yet shared by all the players involved in these technologies. In addition, there are still a number of barriers to overcome if we are to properly anticipate microbial reactivity at depth and the harmful or accelerating effects it could have during these subsurface engineering operations. Given the complexity of the crustal biosphere’s functioning in space and time, pilot site studies are currently among the most instructive sources of observations and knowledge. We will discuss the importance of taking subsurface ecosystems into account during these operations, based on microbiological monitoring carried out on gas storage or geothermal pilot sites.