The improvement of carbon (C) accumulation in soils has been one of the main purposes of the conservation systems in agricultural production. This study aimed to assess the long-term effect of conventional tillage (CT) and no-tillage (NT) combined with winter cover crops, black oat and oilseed radish, and fallow on C accumulation and stabilization in a very clayey Oxisol in Southern Brazil. Soil samples were collected in the 0-0.05, 0.05-0.10 and 0.10-0.20 m layers of a 26-year-old experiment. Distribution of size-class aggregates, C stock in aggregates, total C stock, and C stocks in the physical fractions, free particulate organic matter (free-POM), occluded particulate organic matter (occluded-POM) and mineral-associated organic matter (min-OM) were assessed. NT had a higher percentage of macroaggregates and C stock in this size-class, and also higher C stock in bulk soil, free-POM and occluded-POM fractions than CT in 0-0.05 m (Tukey's test p < 0.05), due to higher input of biomass and minimum soil mobilization in NT. Oat and radish had higher C stock in macroaggregates than fallow in 0.05-0.10 m (Tukey's test p < 0.05). Radish had the highest C stock in the free-POM (0-0.05 m). Fallow decreased the stabilization of macroaggregates and C accumulation in free-POM, due to the lower C input from aboveground biomass over the years. In conclusion, NT after 26 years improved C accumulation and stabilization, mainly in the superficial layer and in POM fractions, and winter cover crops favored the formation and stability of macroaggregates.