A long-term field study was used to compare soil nitrogen and phosphorous status, and soil aggregate stability in organic and conventional cropping systems. Two rotations were tested: a grain only and a grain-alfalfa hay rotation. The organic systems had a lower nitrate leaching potential than the same rotations under conventional management. After 13 years, one organic system (the grain-alfalfa; no manure return) is suffering serious soil P depletion. However, the grain only and the grain-alfalfa with manure return to land systems had soil P levels similar to the prairie grass control treatment and showed no signs of P deficiency. Despite having lower levels of organic carbon, the organic soils had higher levels of wet aggregate stability than conventionally managed soils.