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Soils represent the largest carbon reservoir within terrestrial ecosystems. The mechanisms controlling the amount of carbon stored and its feedback to the climate system, however, remain poorly resolved. Global carbon models assume that carbon cycling in upland soils is entirely driven by aerobic respiration; the impact of anaerobic microsites prevalent even within well-drained soils is missed within this conception. Here, we show that anaerobic microsites are important regulators of soil carbon persistence, shifting microbial metabolism to less efficient anaerobic respiration, and selectively protecting otherwise bioavailable, reduced organic compounds such as lipids and waxes from decomposition. Further, shifting from anaerobic to aerobic conditions leads to a 10-fold increase in volume-specific mineralization rate, illustrating the sensitivity of anaerobically protected carbon to disturbance. The vulnerability of …