Environmental benefits from bioenergy production derived from sugarcane crop residues (straw) can be lost by soil organic matter depletion resulting from excessive straw removal rates from fields. Soil organic carbon stock is the core for sustaining soil health, supporting nutrient cycling, and sequestering carbon dioxide. To find out that how much sugarcane straw can be removed from the field to produce bioenergy without changes in soil C concentrations, we investigated effects of straw removal rates (total, moderate, and no removal of sugarcane straw) on soil carbon and nitrogen fractions in an Oxisol and an Ultisol in southeastern Brazil for two years. Soil C and N fractions were affected by increased rates of straw removal at the second year. In the Oxisol, total straw removal decreased labile and microbial-C by ~30% and soil C stock by 20% compared to no straw removal. No removal decreased microbial-N and total N stock by ~15% and ~20%, respectively. In the Ultisol, no straw removal resulted in increases in C stock by >10% and labile and microbial-C by ~20% related to total straw removal. Total straw removal showed more microbial-N (~10%) and total-N stock (~25%) compared to no straw removal. The moderate straw removal intensity (i.e., 8 to 10 Mg ha−1 of straw) may control the straw-C release to soil by straw decomposition. This study suggests that excessive straw removal rates should be avoided, preventing SOM depletion and consequently, soil health degradation. Moderate straw removal seems to be a promising strategy, but long-term soil C monitoring is fundamental to design more sustainable straw management and bioenergy production systems.