Elevated nutrient deposition often increases primary productivity in terrestrial ecosystems and thus has the potential to increase the flux of carbon (C) into soils. An important step toward greater understanding of nutrient effects on C storage involves assessing effects on different fractions of the soil C pool across a range of soil types. We quantified the combined effects of 8 years of nitrogen (N), phosphorus (P), potassium (K), and micronutrient fertilization on the C storage in bulk soil and in density fractions at four grassland sites in California. When averaged across sites, fertilization increased soil light fraction C by 64% relative to the control in the 0–10 cm depth. The increase in light fraction C likely resulted from the fertilization-induced increase in plant C input to soil, as aboveground net primary productivity also consistently increased with fertilization across sites. Effects of fertilization on heavy fraction C were highly site specific, having positive, negative, or no effect at individual sites. The response of heavy fraction C to fertilization appeared to be related to mean annual precipitation and soil bulk density. Overall, bulk soil C concentration showed a marginally significant increase of 6% with fertilization when averaged across sites (P = 0.07). Our results indicate that biomass production and soil light fraction are generally sensitive to fertilization across grasslands in California, likely contributing to increases in soil C storage. Responses of heavy fraction C, on the other hand, vary greatly among sites and may depend on climate and soil characteristics.