The purpose of this research was to assess the effects of replacement of native "Cerrado" vegetation (NV) into croplands on soil chemical, physical and microbial properties. This research was carried out on a farm under Rhodic Hapludox soil with different types of agricultural managements systems, and it was used a NV to compare the systems. The experimental design was set up in completely randomized with five treatments and five repetitions. The treatments adopted were several agricultural management systems as follow; NV; CS_Crop system; LS_Livestock system; ICLS-4_Integrated crop-livestock system with four years of implementation; ICLS-8_Integrated crop-livestock system with eight years of implementation. It was assessed some chemical, physical, and microbial parameters in the soil, as soil pH, P content, exchangeable cations, cation exchange capacity, base saturation, cations saturation, soil organic carbon (SOC), soil bulk density (SBD), aggregate stability, microbial biomass carbon (MBC), basal breathing, and microbial quotient. The replacement of NV to ICLS decreased SOC, MBC, soil aggregate stability and increase of SBD. The ICLS improved "Cerrado" soil fertility over time adoption. This integrated system increased the quantity of exchangeable K + and P content in "Cerrado" soil. The ICLS-8 showed soil environment nearby the NV. Even the difficulty in obtaining the same physical and microbial condition of NV, the results of this research point out quite important observations, because just no-till system is not enough to obtain improvement of soil quality and the ICLS can return the soil properties close to native "Cerrado" vegetation.