This study helps to assess how variations in the measurement methodology may affect the precision and accuracy of results by portable X-ray fluorescence (XRF) analyser as well as level of sensitivity of XRF for different elements and their concentrations. Under this research the XRF was calibrated, and already prepared soil samples (S0-S4) were analysed for the heavy metals like Cadmium, Cobalt, Chromium, Iron, Manganese, Vanadium, Nickel, Lead and Zinc for different duration of time (10 seconds to 5 minutes) and repetitions (1, 5 and 10) per sample. For each soil sample, a total of 15 XRF analysis tests were conducted and the results for these samples showed noticeable variations in concentration measurements that could be attributed to instrumental or human error, sample homogeneity, or the preparation material used. Based on these observations, analysis for one-minute duration using 10 repetitions per sample was conducted on full-scale for 72 geolocated soil samples from Debrecen by using the same XRF collected from 18 locations at four depth levels (0, 0–20 cm, 20–40 cm, and 40–60 cm).