Soil chemical properties during the transition from conventional to organic and low-input farming practices were studied over 8 yr in California's Sacramento Valley to document changes in soil fertility status and nutrient storage. Four farming systems differing in crop rotation and external inputs were established on land previously managed conventionally. Fertility in the organic system depended on animal manure applications and winter cover crops; the two conventional systems received synthetic fertilizer inputs; the low-input system used cover crops and animal manure during the first 3 yr and cover crops and synthetic fertilizer for the remaining 5 yr. At 4 and 8 yr after establishment, most changes in soil chemical properties were consistent with predictions based on nutrient budgets. Inputs of C, P, K, Ca, and Mg were higher in the organic and low-input systems as a result of manure applications and cover crop incorporations. After 4 yr, soils in the organic and low-input systems had higher soil organic C, soluble P, and exchangeable K. Crop rotation (the presence or absence of corn) also had a significant effect on organic C levels. Differences in total N appeared to be related in part to inputs, but perhaps also to differing efficiency of the farming systems at storing excess N inputs; the low-input system appeared to be most efficient, and the conventional systems were least efficient. Electrical conductivity (EC), soluble Ca, and soluble Mg levels were tightly linked but not consistently different among treatments. Relatively stable EC levels in the organic system indicate that animal manures did not increase salinity. Overall, our findings indicate that organic and low-input farming in the Sacramento Valley result in small but important increases in soil organic C and larger pools of stored nutrients, which are critical for long-term fertility maintenance.