Sustainable agricultural intensificationhas been considered one of the solutions for increasing food production and mitigating climate changes. Nevertheless, soil physical degradation induced by intense mechanization may threaten those benefits in large-scale agricultural regions such as the Brazilian Cerrado. Thus, our study aimed to assess the effects of land use, tillage management, and crop diversification on soil physical quality of two long-term experiments in Cerrado through on-farm visual evaluation of soil structure (VESS) and soil physical parameters. Soil sampling was performed in 0-to-10-and 10-to-20-cm layers of four agricultural systems: soybean [Glycine max (L.) Merr.]-fallow under conventional tillage (SF); soybean-fallow under no-till (SN); soybean-maize (Zea mays L.) succession under no-till (SM); and crop rotation under no-till including soybean, maize, grasses, and legumes (CR). An additional area of native Cerrado vegetation (NV) was included as reference. Land transition from Cerrado to agricultural systems declined the soil physical quality, detected by VESS assessment and physical parameters in both layers. Tillage management did not alter soil physical parameters, which was likely associated with the medium time adoption in the experiments (9 yr) and high resilience capacity of clayey Oxisols. Unexpectedly, SM and CR negatively affected the porosity-and water-associated soil parameters in the 10-to-20-cm layer compared with SN. It suggests that the soil physical damage induced by higher frequency of machinery operations required to manage a more diverse crop sequence may prevail over the benefits provided by crop diversification. Finally, this study highlights that intensified agricultural systems need to be coupled with strategies to reduce and/or control intensive machinery traffic.