The effects of high atmospheric CO2 concentration ([CO2]) on ecosystem processes have been explored using temporal facilities such as open-top-chambers and free-air CO2 enrichment. However, the effects of high [CO2] on soil properties takes decades and may not be captured by short-term experiments. Natural CO2 springs provide a unique opportunity to study the long-term effects of high [CO2]. In this study, we investigated soil properties at a natural CO2 spring. We found that the amounts of total carbon (C) and nitrogen (N) stored in the soil at the high [CO2] site exceeded those in the reference site by 60 and 30%, respectively. The effects of high [CO2] were large in the upper slope position where the canopy openness was high and plants grew faster, but no effects were detected in the lowest position where the canopy openness was lower (half of that at the upper slope position). In contrast, effects of high [CO2] on soil N dynamics, such as N mineralization and nitrification rates, did not exhibit a slope gradient. This suggests that effects of high [CO2] differed among soil stoichiometric characteristics and N dynamics. These complicated effects of high [CO2] imply that the future effects of high [CO2] on ecosystems could vary widely in conjunction with environmental conditions such as light availability and/or topographic conditions.