Conservation Tillage (CT) and cover cropping are sustainable agricultural practices that may provide solutions for California's declining soil, air and water quality. This study looks at the effects of CT and cover cropping on total C and soil organic matter dynamics in a cotton-tomato (Gossypium hirsutum, Lycopersicon esculentum) rotation in California's San Joaquin Valley. After 5 years of treatments, the top 30 cm of soil in the cover cropping system had 4500 kg C/ha more C, while C increased by 3800 kg C/ha in standard tillage. In CT, the increase occurred in the surface 15 cm; while in standard tillage, it was distributed throughout the top 30 cm. In the treatments without cover crops, soil C was unchanged in the 0-30 cm depth. We labeled cotton with 13C in the field and followed the decomposition of both the roots and the shoots through three physical fractions: free particulate organic matter (POM), intra-aggregate POM (iPOM), and mineral associated C. POM tends to turnover quickly while aggregate–protected POM and mineral associated C represent more stable C pools. CT treatments retained more of the cotton residue-derived C in POM and iPOM fractions initially. However, these differences disappear after a year of residue decomposition in the field. During the study, more shoot C was retained and recovered than root C. In California's Mediterranean climate, conservation tillage does not accumulate or stabilize more C than the standard tillage system, and the addition of biomass as a cover crop is more important for total soil C accumulation than tillage practice.