Conservation tillage (CT) and cover cropping (CC) are agricultural practices that may provide solu- tions to address water and air quality issues arising from intensive agricultural practices. This study investigated how CT and CC affect soil organic matter dynamics in a cotton(Gossypium hirsutum L.)-tomato (Lycopersicon esculentum Mill.) rotation in California's San Joaquin Valley. There were four treatments: conservation tillage, no cover crop (CTNO); conservation tillage with cover crop (CTCC); standard tillage, no cover crop (STNO); and standard tillage with cover crop (STCC). After 5 yr, the top 30 cm of soil in CTCC had an increase of 4500 kg C ha−1, compared with an increase of 3800 kg C ha−1 in STCC from initial soil C content in 1999. To enhance our understanding of C dynamics in CT systems, we pulse-labeled cotton with 13CO2 in the fi eld and followed the decomposition of both the roots and the shoots through three physical fractions: light fraction (LF), which tends to turnover quickly, and two relatively stable C pools—intraaggregate LF (iLF) and mineral-associated carbon (mC). Soil under CT treatments retained more of the cotton- residue-derived C in LF and iLF than ST 3 mo after placement in the fi eld. These differences disap- peared after 1 yr, however, with no discernable differences between CT and ST regardless of CC. In California's Mediterranean climate, CT alone does not accumulate or stabilize more C than ST in tomato-cotton rotations, and the addition of cover crop biomass is more important than tillage reduction for total soil C accumulation. Abbreviations: CT, conservation tillage; CTCC, conservation tillage with cover crop; CTNO, conservation tillage, no cover crop; iLF, intraaggregate light fraction; LF, light fraction; mC, mineral- associated carbon; SOM, soil organic matter; ST, standard tillage; STCC, standard tillage with cover crop; STNO, standard tillage, no cover crop.