Soil quality assessments, rarely applied to contaminated soils with metal(loid)s, consider ecological topics such as multifunctionality, resistance and resilience of microbial communities to perturbations, in addition to ecosystem services. In this study, the effect of metal(loid) contamination was evaluated in soils based on physicochemical and biological properties at different distances from an industrial complex and a Cu smelter. From these properties, soil quality indices (SQIs) were tested to compare their sensitivity and relationship with metal(loid) contamination. Enzyme activities and the average well color development, obtained from the community-level physiological profile, were the most suitable soil quality indicators. These variables along with some physicochemical properties [e.g. total organic carbon, pH, and available metal(loid) contents] were selected to develop SQIs. Five SQIs were calculated, from which the Multifunctionality assessment and the AreaSQI were found to be suitable methods to develop SQIs due to their higher discriminant power and relationship with metal(loid) contamination compared to other SQIs. They were validated using data from the literature, and both showed decreasing values at higher levels of metal(loid) contamination. Although the AreaSQI represents an attractive approach due to its visualization and easy interpretation, the multifunctionality approach showed a stronger sensitivity to chemical degradation by metal(loid)s in soil and offered an easier and faster calculation alternative.