The way we farm affects the buildup and composition of soil organic matter. Our concept of organic matter protection has become more sophisticated, but the extent to which crop nutrients can be supplied by labile soil organic matter is still unknown. A better understanding of nitrogen availability as a result of different management practices, and the relationship between management, dynamic soil properties, and need for nitrogen additions will allow for more precise nitrogen recommendations. The objectives of this study were to: (i) evaluate the effect of management on organic matter, (ii) determine an optimum N rate for corn in each cropping system, and (iii) explore the relationship between soil organic matter measurements and the optimum N rate. The study was conducted within the Wisconsin Integrated Cropping Systems Trial, which includes six common Wisconsin cropping systems. Soil samples were collected in the spring and analyzed for particulate organic matter (POM). Fall soil samples were fractionated and C and N were measured in each aggregate fraction.  Nitrogen was applied at different rates to the corn phase of three systems to determine an optimum N rate. Rotations including perennial crops were significantly enriched in total soil organic matter as well as POM. Although POM content did not differ between systems, POM was significantly depleted in C and N under organically managed corn. Organic corn has less aggregates by weight but is enriched in N in the silt& clay fractions. Continuous corn had increased nitrogen in microaggregates within macroaggregates, likely a result of increased inputs adding fresh residue and encouraging macroaggregate formation. Under drought conditions in SW Wisconsin, both the strip-till corn and organic corn out-performed continuous corn in yield, with similar N uptake in each system. These results show that increased inputs and decreased tillage both increase soil N retention.