The sugarcane in Brazil is passing through a management transition that is leading to theabolition of pre-harvest burning. Without burning, large amounts of sugarcane trash is gen-erated, and there is a discussion regarding the utilization of this biomass in the industryversus keeping it in the field to improve soil quality. To study the effects of the trash removalon soil quality, we established an experimental sugarcane plantation with different levelsof trash over the soil (0%, 50% and 100% of the original trash deposition) and analyzed thestructure of the bacterial and fungal community as the bioindicators of impacts. The soilDNA was extracted, and the microbial community was screened by denaturing gradient gelelectrophoresis in two different seasons. Our results suggest that there are no effects fromthe different levels of trash on the soil chemistry and soil bacterial community. However,the fungal community was significantly impacted, and after twelve months, the communitypresented different structures among the treatments.