To mitigate climate change, some seek to store carbon from the atmosphere in agricultural soils. However, our understanding about how agriculture affects soil organic carbon is muddied by studies lacking longitudinal data, ignoring bulk density changes, or sampling only surface soils. To better understand soil organic carbon trends, here we measured changes over 30 years in density-corrected, full-soil-depth (90 cm) soil organic carbon stocks under 6 cropping systems and a restored prairie in a Mollisol of southern Wisconsin, USA. Cash-grain systems and alfalfa-based systems lost soil organic carbon. Prairie and rotationally-grazed pasture maintained soil organic carbon. Average soil organic carbon losses for cash-grain and alfalfa-based systems were −0.82 (±0.12) and −0.64 (±0.17) Mg C ha−1 yr−1, respectively. Sensitivity analysis showed that incomplete methodologies overestimated soil organic carbon improvements. Our findings using more comprehensive methods demonstrate the inadequacy of row-crop systems and the need for well-managed grasslands to protect soil organic carbon in productive agricultural soils of the Upper Midwest USA.