Growing global demand for bioenergies has raised the interest in using sugarcane crop residues (straw) as feedstock to produce cellulosic ethanol and/or bioelectricity in Brazil. However, indiscriminate straw removal may deplete soil quality, particularly induced by its negative effects on soil microbial communities. A 2-year field study was conducted in soils classified as Oxisol (site 1) and Ultisol (site 2) in southeastern Brazil. The experiment started after plant cane cycle, establishing three straw removal rates (treatments), as follows: total removal, moderated removal, and no removal of sugarcane straw from the field. The amount of straw left on the soil surface and removed in the treatments varied according to the straw yield of each year and location. Soil samples were collected at 0-5- and 5-10-cm layers. The total abundance of bacteria, archaea, and fungi were analyzed by real-time quantitative polymerase chain reaction (qPCR). Bulk density, pH, base saturation, cation exchange capacity, phosphorus (P), and total organic C and soil microbial biomass C (MBC) were also measured. The soil chemical results indicate that the Oxisol presents higher inherent soil fertility compared with the Ultisol. In the first year, the straw had a different significant effect for bacterial and archaeal abundance in both soils and for fungi in the Oxisol site. In the second year, the numbers of gene copies of bacteria, archaea, and fungi in the 0-5-cm layer were higher under moderated and no removal when compared with those under total removal, regardless of site. The MBC decreased significantly under total removal of straw at the Ultisol site. Moderate straw removal has no significant effect on the abundance of soil microbes, but total straw removal may induce sharp reductions (from 23 to 54\%) on microbial abundance. Soil microbes are a sensitive indicator to assess soil changes induced by crop residue management and should be taken into account for defining sugarcane straw management towards a sustainable bioenergy production.