The introduction of crop management practices after conversion of Amazon Cerrado into cropland influences soil C stocks and has direct and indirect consequences on greenhouse gases (GHG) emissions. The aim of this study was to quantify soil C sequestration, through the evaluation of the changes in C stocks, as well as the GHG fluxes (N 2O and CH 4) during the process of conversion of Cerrado into agricultural land in the southwestern Amazon region, comparing no-tillage (NT) and conventional tillage (CT) systems. We collected samples from soils and made gas flux measurements in July 2004 (the dry season) and in January 2005 (the wet season) at six areas: Cerrado, CT cultivated with rice for 1 year (1CT) and 2 years (2CT), and NT cultivated with soybean for 1 year (1NT), 2 years (2NT) and 3 years (3NT), in each case after a 2-year period of rice under CT. Soil samples were analyzed in both seasons for total organic C and bulk density. The soil C stocks, corrected for a mass of soil equivalent to the 0–30-cm layer under Cerrado, indicated that soils under NT had generally higher C storage compared to native Cerrado and CT soils. The annual C accumulation rate in the conversion of rice under CT into soybean under NT was 0.38 Mg ha −1 year −1. Although CO 2 emissions were not used in the C sequestration estimates to avoid double counting, we did include the fluxes of this gas in our discussion. In the wet season, CO 2 emissions were twice as high as in the dry season and the highest N 2O emissions occurred under the NT system. There were no CH 4 emissions to the atmosphere (negative fluxes) and there were no significant seasonal variations. When N 2O and CH 4 emissions in C-equivalent were subtracted (assuming that the measurements made on 4 days were representative of the whole year), the soil C sequestration rate of the conversion of rice under CT into soybean under NT was 0.23 Mg ha −1 year −1. Although there were positive soil C sequestration rates, our results do not present data regarding the full C balance in soil management changes in the Amazon Cerrado.