Understanding the dynamics and distribution of CO2 in the subsurface atmosphere of carbonate karst massifs provides important insights into dissolution and precipitation processes, the role of karst systems in the global carbon cycle, and the use of speleothems for paleoclimate reconstructions. We discuss long-term microclimatic observations in a passage of Postojna Cave, Slovenia, focusing on high spatial and temporal variations of pCO2. We show 1) that the airflow through the massif is determined by the combined action of the chimney effect and external winds and 2) that the relationship between the direction of the airflow, the geometry of the airflow pathways, and the position of the observation point explains the observed variations of pCO2. Namely, in the terminal chamber of the passage, the pCO2 is low and uniform during updraft, when outside air flows to the site through a system of large open galleries. When the airflow reverses direction to downdraft, the chamber is fed by inlets with diverse flow rate and pCO2, which enter via small conduits and fractures embedded in a CO2-rich vadose zone. If the spatial distribution of inlets and outlets produces minimal mixing between low and high pCO2 inflows, high and persistent gradients in pCO2 are formed. Such is the case in the chamber, where vertical gradients of up to 1000 ppm/m is observed during downdraft. The results presented in this work provide new insights into the dynamics and composition of the subsurface atmosphere and demonstrate the importance of long-term and spatially distributed observations.