Continuous measurements of soil CO2 flux are useful for understanding degassing processes and for monitoring volcanic activities. Recent studies at many volcanoes have revealed that soil CO2 flux variations are significantly influenced by environmental parameters as well as volcanic processes. In this study, we conducted continuous monitoring of soil CO2 flux in the flank of Nakadake cone, Aso volcano, Japan, from January 2016 to November 2017. The results of our observations during an active period before and after a large phreatomagmatic eruption on 8 October 2016 and during a calm period from 2017 showed variations in soil CO2 flux due to oscillations in environmental parameters. Excluding these variations from the raw time series by multivariate linear regression analysis, the time series of soil CO2 flux presented some anomalous peaks in both the active and calm periods. Careful comparison of the anomalous peaks with the environmental parameters revealed that most of the anomalous peaks were likely due to an increase in wind speed and/or a decrease in barometric pressure. However, the anomaly after the 8 October 2016 eruption was not completely explicable by the variations in the environmental parameters and coincided with increases in seismic amplitude and plume SO2 flux. This anomaly was possibly attributed to an increase in magmatic CO2 flux. These findings emphasized the importance of careful statistical treatment of the soil CO2 flux data after excluding the influences of the environmental parameters at each measurement site. These statistical treatments will contribute to a better understanding of the degassing processes and monitoring of volcanic activities, including phreatic or phreatomagmatic eruptions.