Sugarcane is the main crop used in ethanol biofuel production in Brazil and it may be harvested with or without burning, increasing or decreasing greenhouse gases emissions and soil carbon deposition. In this study, we evaluated the effect of the sugarcane harvest system (with and without burning, at one, three, and six years after the last replanting) on C contents and C stocks in the soil, the physical quality of soil organic matter, and C immobilization in soil microbial biomass. The areas harvested without burning showed higher C content in the surface layer and higher C stocks, regardless of the time after the last replanting. Differences in the physical quality of organic matter mainly occurred in the 53 to 75 µm particle size fraction, in which the C ratio was higher in the unburned areas. In the 0-10 cm layer, harvesting without burning was associated with higher microbial C. Harvest without straw burning is effective in accumulating C in forms with long residence time in the soil.