Opposite to atmospheric CO2 concentrations, which reach a minimum during the vegetation season (e.g., June–August in the Northern Hemisphere), soil CO2 reaches a maximum in the same period due to the root respiration. In karst areas, characterized by high rock porosity, this excess CO2 seeps inside caves, locally increasing pCO2 values above 1%. To better understand the role of karst areas in the carbon cycle, it is essential to understand the mechanisms of CO2 dynamics in such regions. In this study, we present and discuss the spatial and temporal variability of air temperature and CO2 concentrations in Samograd Cave, Croatia, based on three years of monthly spot measurements. The cave consists of a single descending passage, resulting in a characteristic bimodal climate, with stable conditions during summer (i.e., stagnant air inside the cave) and a strong convective cell bringing in cold air during winter. This bimodality is reflected in both CO2 concentrations and air temperatures. In summer, the exchange of air through the cave’s main entrance is negligible, allowing the temperature and CO2 concentration to equilibrate with the surrounding rocks, resulting in high in-cave CO2 concentrations, sourced from enhanced root respiration. During cold periods, CO2 concentrations are low due to frequent intrusions of fresh external air, which effectively flush out CO2 from the cave. Both parameters show distinct spatial variability, highlighting the role of cave morphology in their dynamics. The CO2 concentrations and temperatures have increased over the observation period, in line with external changes. Our results highlight the role of caves in transferring large amounts of CO2 from soil to the atmosphere via caves, a process that could have a large impact on the global atmospheric CO2 budget, and thus, call for a more in-depth study of these mechanisms.