Energy crops are industrial species that can generate energy, biofuels and bioproducts. The soils that should be most adequate to cultivate energy crops in mainland Portugal are marginal, degraded and contaminated soils avoiding Indirect Land Use Change (ILUC) burdens. Based on a previous study that mapped the marginal areas of mainland Portugal, using tools and baseline documents and ArcGIS software as a Geographic Information System (GIS) tool, three specific areas were subsequently selected to implement energy crops. This work aims to present the soil characterization of the chosen areas (pH, electrical conductivity, sand, clay and silt, total phosphorus and nitrogen content, etc.), to identify additional constraints for the cultivation of the energy crops not foreseen in the modeling and to validate the model used. Among the different marginal areas identified by the model, the three soils chosen to correspond to three regions with different edaphoclimatic conditions of mainland Portugal, namely, Braga in the north (region with high precipitation), Loures in the Metropolitan area of Lisbon and Mértola, further south, specifically at São Domingos Mine. Based on the marginal map obtained, the Braga soil is slightly acidic, with a pH of 4.87 and slopes between 16 and 25%, Loures soil has a topsoil containing 52% clay and São Domingos Mine is acidic (pH = 3.94). In each of the three selected areas, the soil was collected and then characterized. Results obtained on the analysis of the collected soils show that the model used to map the marginal soils is validated.