Soil turning during pre-seeding preparation is meant to loosen and promote physical characteristics responsible for the development of crop roots in soil. In this study, we demonstrate effects of three methods of pre-seeding preparation at two depths of irrigation on carbon dioxide (CO2) efflux as well as the temporal variability in the distribution of soil carbon. This experiment was conducted at the rural cooperative extension research station in Tangará da Serra, Mato Grosso, Brazil, for two wheat production years in 2011 and 2012. The experimental design was randomized in strips, with four repetitions. Wheat was irrigated during the June to early October dry season. The treatments include two methods of soil preparation: traditional preparation with one plowing and two disc harrowings and minimal preparation with one seed bed conditioner pass. A third treatment of direct seeding was also evaluated. Soil CO2 efflux, soil temperature, air-filled soil porosity, and labile carbon were measured. We found soil preparation affects CO2 efflux in irrigated cultivation systems within Brazil’s Cerrado savannah, with conventional tillage having greater CO2 emissions than either reduced tillage or direct seeding. Soil CO2 emissions were lower at 508 mm versus 698 mm irrigation depth, but wheat yields were significantly lower.