The Long-Term Agroecological Research (LTAR) site was established in 1998 on the Neely-Kinyon Research Farm near Greenfield, Iowa to evaluate agronomic and economic outcomes of certified organic and conventional grain-based cropping systems. The site was certified organic in 2000. This study evaluates changes in soil quality during and after transition from conventionally managed corn and soybeans to organically managed soy- and corn-based rotations containing small grains and forage legumes amended with composted swine manure. Experimental design is completely randomized with 4 replications. Surface soil samples (0-15 cm) were collected after harvest from 1998 through 2006. We quantified total soil organic carbon (SOC) and nitrogen (TN), microbial biomass C (MBC), particulate organic matter C (POM C), potentially mineralizable N (PMIN N), stable macroaggregates, nitrate and ammonium N, Bray P, ammonium acetate extractable K, Mg, and Ca, electrical conductivity (EC), pH, and bulk density. MBC and Bray P were higher in the organic rotations after one growing season, reflecting the application of composted swine manure in spring 1998. MBC, POM C, PMIN N, Bray P, and pH were greater in the organic rotations in the fall of 2001, and by the end of the 2004 growing season SOC, TN, and macroaggregate stability (indicator of erosion potential) were greater in the organic systems and BD and EC (indicator of soil salinity) did not differ among the systems. Soil nitrate N and the nitrate-N:PMIN N ratio were consistently higher in the conventional system, starting at the end of the first growing season, indicating a lower potential for N leaching loss in the organic system. Our data indicate overall soil quality is enhanced in organic rotations and suggest organic management may enhance soil function to maintain agronomic productivity and increase environmental buffering capacity of the soil.