Current soil C inventories focus on surface layers although over half of soil C is found below 20 cm. Recent and ongoing changes in agricultural management, crop productivity, and climate in Midwest US cropland may influence subsoil C stocks. The objectives of this study were to determine how surface soil and subsoil organic C stocks have changed in croplands of Iowa and Illinois and to evaluate mechanisms to explain the observed subsoil organic C changes. Using resampling studies from Iowa and Illinois, we found that subsoil (20-80 cm) organic C increased at a rate of 0.31 Mg C ha-1 yr-1 between the 1950s and early 2000s despite C losses of similar magnitude in the top 20 cm (0.26 Mg C ha-1 yr-1). Based on this analysis, we estimated a subsoil C storage rate of up to 11.8 Tg C yr-1 for Iowa and Illinois, which equates to 12% of annual US greenhouse gas emissions from crop cultivation if surface C losses and non-CO2 greenhouse gases are controlled. We also measured changes in soil organic C stocks from two long-term cropping systems experiments located in Iowa, which demonstrated similar rates of subsoil C changes for both historical and contemporary crop rotations. Using publicly available crop yield data, we determined that changes in crop productivity likely contributed minorly to observed changes in subsoil organic C. The accumulation of organic C in subsoils may be attributed to regional climate change, which has led to greater precipitation and wetter subsoils that inhibit transformation of soil organic C to CO2. Because farmers may respond to increasing soil wetness by expanding and intensifying artificial drainage infrastructure, there is an urgent need to further assess subsoil C stocks and their vulnerability to drainage system changes.