Soil aggregate and particulate organic matter (POM) C and N provide valuable insight into C cycling and storage, and are sensitive to management, but effect of these pools on corn yield is unknown. Corn yield, N uptake, and aggregate and POM C and N at 0-5, 5-25 and 25-50 cm were measured and correlated in continuous corn (Zea mays L.) (CC), strip-till corn/soybean [Glycine max (L.) Merr.] (CS), and organically managed corn/soybean/wheat (Triticum aestivum L.) with green manure (CSW). The POM differed only at 0-5 cm, where greater POM mass was found in CS than CC and CSW. Lower POM-C and POM-N was found in CSW than CC and CS. Overall, CSW had fewer macroaggregates (> 250 mu m) and associated C and N than CC and CS, but free silt and clay (< 53 mu m) and microaggregates (53-250 mu m) were enriched in C and N in CSW. Yield and macroaggregate-occluded C and N were negatively correlated. Yield and 5-25 cm free silt and clay C were positively correlated. While organic matter in aggregate-occluded fractions is beneficial for soil C storage, it was correlated with lower grain yields, highlighting a potential tradeoff between yield and long-term C sequestration.