Data presented are on carbon (C) and nitrogen (N) inputs, and changes in soil C and N in eight systems during the first eight years of a tillage-intensive organic vegetable systems study that was focused on romaine lettuce and broccoli production in Salinas Valley on the central coast region of California. The eight systems differed in organic matter inputs from cover crops and urban yard-waste compost. The cover crops included cereal rye, a legume-rye mixture, and a mustard mixture planted at two seeding rates (standard rate 1x versus high rate 3x). There were three legume-rye 3x systems that differed in compost inputs (0 versus 7.6 Mg ha−1 vegetable crop−1) and cover cropping frequency (every winter versus every fourth winter). The data include: (1) changes in soil total organic C and total N concentrations and stocks and nitrate N (NO3-N) concentrations over 8 years, (2) cumulative above ground and estimated below ground C and N inputs, cover crop and crop N uptake, and harvested crop N export over 8 years, (3) soil permanganate oxidizable carbon (POX-C) concentrations and stocks at time 0, 6 and 8 years, and (4) cumulative, estimated yields of lettuce and broccoli (using total biomass and harvest index values) over the 8 years. The C inputs from the vegetables and cover crops included estimates of below ground inputs based on shoot biomass and literature values for shoot:root. The data in this article support and augment information presented in the PLoS ONE research article “Winter cover crops increase readily decomposable soil carbon, but compost drives total soil carbon during eight years of intensive, organic vegetable production in California”. Resources in this dataset:Resource Title: Supplementary materials. File Name: Web Page, url: https://ars.els-cdn.com/content/image/1-s2.0-S2352340920313639-mmc1.zip Zipped Excel (xlsx) data comprising Supplementary Table 1: Raw data of soil total organic carbon concentrations, total nitrogen concentrations, nitrate nitrogen concentrations, total organic carbon stocks, and total nitrogen stocks over 8 years from the Salinas Organic Cropping Systems experiment in Salinas, California. This includes data from all eight systems in the experiment. The related article in PLoS ONE only included data from five of the eight systems with optimal seeding rates for weed suppression. Supplementary Table 2: Raw data of cumulative cover crop and vegetable carbon inputs, legume nitrogen fixation, cover crop and vegetable crop N uptake and export during 8 years at the Salinas Organic Cropping Systems experiment in Salinas, California. This includes data from all eight systems in the experiment. The related article in PLoS ONE only included data from five of the eight systems with optimal seeding rates for weed suppression. Supplementary Table 3: Raw data of soil permanganate oxidizable carbon (POX-C) concentrations and stocks at the 0 to 6.7 cm depth in years 0 and 6, and the 0 to 30 cm depth in year 8 from the Salinas Organic Cropping Systems experiment in Salinas, California This data from five of the eight systems with optimal seeding rates for weed suppression was included the related paper in PLoS ONE. Supplementary Table 4: Raw data of cumulative, estimated yields of lettuce and broccoli crop during 8 years at the Salinas Organic Cropping Systems experiment in Salinas, California; yields are on an oven-dry basis. This includes data from all eight systems in the experiment.