Urban agricultural soils have important social, environmental, and economic roles in big cities, contributing to their sustainability. However, food production in urban soils may be compromised due to soil pollution that resulted from decades of industrial, non-regulated environmental activity and mobile transport. In this study, 12 soils from the urban agricultural area of Rome (Italy) were analyzed for the potentially toxic elements (PTEs) Be, Ba, Pb, Co, Ni, V, Zn, Hg, Cd, As, Cu, and Cr. All but one of the soils under analysis were characterized by at least one PTE concentration above the threshold limit defined by the D.Lgs 152/06 for agricultural soils. Multivariate analysis showed that the soils could be classified into five clusters: clusters I and II had relatively lower mean PTE concentrations; clusters III, IV, and V had relatively higher mean PTE concentrations with several PTE concentrations above the threshold proposed by ILD. Three factors contributing to the variability of the PTE’s concentration in the soils under investigation were identified: a geological factor related to PTE As, Ba, Be, and V; an anthropogenic factor related to Pb and Cu; and a mixed factor related to Co, Cr, Ni, and Zn. High PTE content may limit the utilization of urban soils for food production.