In soil pollution studies, large numbers of soil samples collected at random need to be processed and analyzed to determine their heavy metal contents. This study was designed to assess the use of a field portable X-ray fluorescence (FPXRF) spectrometry system for the in situ determination of heavy metal levels in both soil and plant samples. First, we optimised the method using 84 reference soil standards and soil samples from known polluted sites. The optimised method was then used to determine heavy metals at three abandoned mine sites and two sealed landfills in central Spain. Given that knowledge of heavy metal levels in plants is important for the ecotoxicological study of these sites, the FPXRF device was also used to determine heavy metals in plants. Our results indicate the acceptable to high quality of the data provided by the system especially for soil samples. The cost-benefits and sustainability of this instrument in relation to other techniques were also examined. The use of the FPXRF system for the study of potentially polluted sites was found to save on costs, time and materials. Results indicate its suitable use for the preliminary screening of heavy-metal polluted sites.