The determination of the contribution of background values in a potentially polluted soil is very important in defining the contamination extension, in particular in areas of geological complexity and long-term economic development, where mining and industry have been traditional activities and soils are showing both geogenic and anthropogenic contributions. Some approaches have been proposed for the estimation of the anthropogenic input vs. the background; in this paper we present a more robust approach. The proposed methodological approach includes the following steps. The first step consists of the comparison among the trace element contents in potentially polluted soils (PPS) and the reference and threshold values calculated both for the same geotectonic unit. A second stage is the calculation of the reference and threshold values for the surrounding area (LTV), natural setting, of the PPS with similar lithological characteristics. The final step is based on the analysis of the results by comparison of the PPS with LTV. On the other hand, the definition of a new pollution factor allows to grade the pollution and to classify the pollution importance. The protocol proposed was applied to PPS from a potentially polluted area of SW Spain. The anthropogenic vs. geogenic anomalies and the pollution grade of the three PPS were assessed, which is important to establish the priority to further actions. In addition, this study makes clear that the use of the enrichment factors to estimate the pollution of soils is not advisable. On the other hand, in this study, new areas close to the PPS were defined as potentially polluted because of the high trace element concentration. The methodological approach proposed can be considered as a good indicator for evaluating the geogenic vs. anthropogenic contribution in polluted soils and for classifying the pollution importance in a more robust way than the use of other previous indexes. The proposal methodology could be used also by the administration to detect other PPS in a study area, which a priori were not considered as contaminated.