<p>Soil contamination caused by human activities is a global concern impacting food security and the practice of sustainable agriculture, in alignment with the UN’s sustainable development goals. Therefore, it is vital to map potentially toxic elements (PTEs) in soils quickly and without causing pollution to outline actions for mitigating their negative environmental impact. In this sense, magnetic susceptibility (MS) emerges as a promising indirect technique for predicting PTE concentrations, as it is closely linked to key pedoindicator attributes such as soil mineralogy, iron oxide content, particle-size distribution, and the accumulation of ferrimagnetic particles derived from both natural and anthropogenic processes. These relationships allow MS to reflect changes in soil properties that are often associated with the presence and spatial variability of potentially toxic elements. This study aimed to estimate PTEs in soils using MS measurements, assess PTE contents in soils under sugarcane cultivation, and understand the anthropic influence on their presence in the studied soils. Soil samples were collected in a transition area of soils originating from basalt, Botucatu sandstone, and colluvium-eluvium deposits. Particle size, chemical, and mineralogical analyses and MS measurements were conducted. The data were analyzed using descriptive statistics, Pearson correlation, multiple linear regression, and pedotransfer functions were used to estimate PTEs using MS. PTE prediction models were satisfactorily calibrated using MS and clay for the elements Co, Cr, Cu, Ni, and Pb (R² &gt; 0.59). PTEs showed spatial dependence and were positively correlated with iron oxides and SM. The metals Co, Cu, and Ni presented contents above the quality reference values in basalt soils, including in the analyzed points in the native forest under basalt. The presence of PTEs in soils is strongly related to their concentrations in the parent material.</p>