We investigated the effects of three elevated atmospheric CO2 levels on a Populus deltoides plantation at Biosphere 2 Laboratory in Oracle Arizona. Stable isotopes of carbon have been used as tracers to separate the carbon present before the CO2 treatments started (old C), from that fixed after CO2 treatments began (new C). Tree growth at elevated [CO2] increased inputs to soil organic matter (SOM) by increasing the production of fine roots and accelerating the rate of root C turnover. However, soil carbon content decreased as [CO2] in the atmosphere increased and inputs of new C were not found in SOM. Consequently, the rates of soil respiration increased by 141% and 176% in the 800 and 1200 μL L−1 plantations, respectively, when compared with ambient [CO2] after 4 years of exposure. However, the increase in decomposition of old SOM (i.e. already present when CO2 treatments began) accounted for 72% and 69% of the increase in soil respiration seen under elevated [CO2]. This resulted in a net loss of soil C at a rate that was between 10 and 20 times faster at elevated [CO2] than at ambient conditions. The inability to retain new and old C in the soil may stem from the lack of stabilization of SOM, allowing for its rapid decomposition by soil heterotrophs.