To better understand agricultural carbon fluxes in California, USA, we estimated changes in soil carbon and woody material between 1980 and 2000 on 3.6 × 106 ha of farmland in California. Combining the CASA (Carnegie-Ames-Stanford Approach) model with data on harvest indices and yields, we calculated net primary production, woody production in orchard and vineyard crops, and soil carbon. Over the 21-yr period, two trends resulted in carbon sequestration. Yields increased an average of 20%, corresponding to greater plant biomass and more carbon returned to the soils. Also, orchards and vineyards increased in area from 0.7 × 106 ha to 1.0 × 106 ha, displacing field crops and sequestering woody carbon. Our model estimates that California's agriculture sequestered an average of 19 g C·m−2·yr−1. Sequestration was lowest in non-rice annual cropland, which sequestered 9 g C·m−2·yr−1 of soil carbon, and highest on land that switched from annual cropland to perennial cropland. Land that switched from annual crops to vineyards sequestered 68 g C·m−2·yr−1, and land that switched from annual crops to orchards sequestered 85 g C·m−2·yr−1. Rice fields, because of a reduction in field burning, sequestered 55 g C·m−2·yr−1 in the 1990s. Over the 21 years, California's 3.6 × 106 ha of agricultural land sequestered 11.0 Tg C within soils and 3.5 Tg C in woody biomass, for a total of 14.5 Tg C statewide. This is equal to 0.7% of the state's total fossil fuel emissions over the same time period. If California's agriculture adopted conservation tillage, changed management of almond and walnut prunings, and used all of its orchard and vineyard waste wood in the biomass power plants in the state, California's agriculture could offset up to 1.6% of the fossil fuel emissions in the state.