This is the first study involving both controlled and replicated comparison of the soil quality and resulting performance of identically-managed cropping systems (differing only in the duration of organic management). Tomato growth and yield in both first-year transitional and established (sixth-year) organic plots exceeded that in the most directly comparable conventional plots, apparently because field operations during wet spring conditions caused more damage to the soil structure in the conventional system. Soil nitrate nitrogen remained stable throughout the season in the established organic and transitional plots, indicating that the microbial populations necessary for mineralization in the transitional system were present and effective despite its history of conventional management. On two dates during the first growing season, microbial populations in the established organic plots were intermediate (as shown by canonical analysis) between the conventional and transitional plots. Samples are still being collected and analyzed for the second year of the rotation, in which all plots are in field corn.