Sequestration of carbon dioxide (CO2) in geological formations is a crucial challenge for reducing anthropogenic greenhouse gases and for ensuring an effective solution toward a sustainable energy transition at net zero emissions. In the framework to assess the potential risk associated with gas leakage from underground storage sites, natural analogues represent ideal places for studying gas migration through the Earth’s critical zone. The aim of this paper has been to investigate the natural gas release from karst environment in order to understand how CO2 may migrate within the vadose zone and to predict its behavior. For this purpose, standard micrometeorological techniques have been used in a 100 m-deep cave in NW Sardinia (Italy) for measuring CO2 dynamic at the geosphere-atmosphere interface. The monitoring system was installed at the near-surface and optimized for recording continuously cave CO2 dynamic together with the main meteorological parameters. The results show that the temporal variation in gas concentration can be explained by two main mechanisms related to atmospheric variables: (1) the barometric pressure pumping and, with minor contribution, (2) the thermal-induced convection. The research also suggests that near-surface measurements inside caves could help in developing, testing, and optimizing different monitoring platforms capable of detecting gas emissions even at concentration close to atmospheric values.