Soil microbial biomass represents an important and strategic reservoir of plant nutrients that can be quickly altered due to different soil and crop managements. In this context, the aim of this study was to evaluate the influence of sugarcane harvesting systems, with or without burning, on the chemical and biological properties of the soil. The experiment was conducted on a dystrophic red latosol (Oxisol) soil in 2008, in a commercial area of a sugarcane factory in the municipality of Paraguaçu Paulista, São Paulo state, Brazil. The treatments included areas previously burned, areas with mechanical harvesting and no burning and native forest. Soil samples were collected immediately after the sugarcane harvest from the treatments at a depth of 0–20 cm. The parameters evaluated were: microbial biomass C and N (MB-C and MB-N), total organic C (TOC), recalcitrant C (R-C), labile-C (L-C), total nitrogen (TN), pH, exchangeable cations (Ca2 + + Mg2 + and K+), exchangeable (Al3+) and potential (H+ + Al3+) acidity, and P available in the soil. Soil chemical fertility under the sugarcane without burning was better than under sugarcane with burn. The TOC values for native forest and for the harvesting without burn were higher than those under the sugarcane with burn (148% and 54%, respectively). This superiority was also confirmed for TN, L-C and R-C. An even more significant difference was found under natural forest and sugarcane without burn for MB-C, which was 222% higher under native forest and 102% higher under sugarcane without burn than the value under sugarcane with burn, confirming that MB-C could be a reliable indicator of soil quality for monitoring soils under different sugarcane harvesting systems.