Isolating soil organic carbon (SOC) from soil inorganic carbon (SIC) is necessary to quantify SOC stocks and understanding SOC dynamics. Inorganic acids are commonly used to remove SIC and several methods have been developed to minimize the impacts these acid treatments have on the residual SOC. Negative impacts on the SOC pool, such as underestimating SOC stocks, are caused in part due to differences in the amount and composition of the organic matter pool. The effects of SIC removal on SOC are often ignored within experimental studies based on the assumption that soils from the same site do not differ enough to impact results. However, some experimental treatments, such as elevated atmospheric CO 2 , change SOC pools in both concentration and composition. Therefore, SIC removal can introduce different biases in control and treatment soils that may differ by method. In this work, we compare two commonly used methods of SIC removal on a set of soil samples from the same elevated CO 2  experiment. We use soils from the Nevada Desert Free Air Carbon dioxide Enrichment Facility to quantify how SIC removal with either acid washing or acid fumigation affect SOC in control and elevated CO 2 plots. We then use the difference in SOC (%C and δ 13 C) between methods to infer changes in the SOC pool driven by the elevated CO 2 treatment. Our results show that acid washing underestimates SOC relative to fumigation and that this difference is larger in soils from control CO 2 plots than elevated CO 2 plots. This may suggest that stabilization mechanisms sensitive to acidification, such as calcium bridging, are disrupted under elevated CO 2 treatment and therefore are less susceptible to SOC loss during acid washing. Our results present future research avenues for exploring the effects of acidic organic compounds, such as root exudates, on SOC stability in alkaline soils.