The increasing concentration of CO2 in the atmosphere is perturbing the global carbon (C) cycle, altering stocks of organic C, including soil organic matter (SOM). The effect of this disturbance on soils in arid ecosystems may differ from other ecosystems due to water limitation. In this study, we conducted a density fractionation on soils previously harvested from the Nevada Desert FACE Facility (NDFF) to understand how elevated atmospheric CO2 (eCO2) affects SOM stability. Soils from beneath the perennial shrub, Larrea tridentata, and from unvegetated interspace were subjected to a sodium polytungstate density fractionation to separate light, particulate organic matter (POM, <1.85 g/cm3) from heavier, mineral associated organic matter (MAOM, >1.85 g/cm3). These fractions were analyzed for organic C, total N, δ13C and δ15N, to understand the mechanisms behind changes. The heavy fraction was further analyzed by pyrolysis GC/MS to assess changes in organic compound composition. Elevated CO2 decreased POM‐C and MAOM‐C in soils beneath L. tridentata while interspace soils exhibited only a small increase in MAOM‐N. Analysis of δ13C revealed incorporation of new C into both POM and MAOM pools indicating eCO2 stimulated rapid turnover of both POM and MAOM. The largest losses of POM‐C and MAOM‐C observed under eCO2 occurred in soils 20–40 cm in depth, highlighting that belowground C inputs may be a significant driver of SOM decomposition in this ecosystem. Pyrolysis GC/MS analysis revealed a decrease in organic compound diversity in the MAOM fraction of L. tridentata soils, becoming more similar to interspace soils under eCO2. These results provide further evidence that MAOM stability may be compromised under disturbance and that SOC stocks in arid ecosystems are vulnerable under continued climate change. We separated soils from a long‐term elevated atmospheric CO2 experiment into less‐stable and more‐stable pools of organic matter. We found a decrease in organic carbon from both pools in soils beneath the dominant perennial shrubs, Larrea tridentata, indicating that elevated CO2 stimulated decomposition. Using stable isotope analysis, we also show that new organic carbon is incorporated into the more‐stable pool of organic matter. These results demonstrate that elevated CO2 disrupts and possibly accelerates soil carbon cycling in arid ecosystems, leading to a loss of stable organic carbon in soils under some perennial vegetation cover types.