According to the Scopus database, over the last five years, 91 scientific papers with the keyword “pXRF” (portable X-ray fluorescence) were published in indexed journals in the domain of environmental science and agricultural science, which indicates more frequent applications of this technique in scientific research. The pXRF method is characterized by speed, precision, accuracy, and the possibility of a simultaneous analysis of a large number of elements, albeit with higher limits of detection (LODs) as a major disadvantage. The presence of metals in certain phosphate fertilizers is well established, though not to the same extent as in mineral nitrogen fertilizers. The aim of this research was to determine the metal content (As, Cd, Co, Cr, Cu, Fe, Mn, Mo, Ni, Pb, Si, Sr, Th, U, Zn, Zr, and Y) in thirteen commercial mineral nitrogen fertilizers via the pXRF method. Six straight fertilizers (ammonium nitrate, ammonium sulphate nitrate, limestone ammonium, nitrate, and urea) and seven complex fertilizers (various NPK formulations), which are different even according to their production technology, produced in Croatia were analyzed using the handheld Vanta C (Olympus) XRF analyzer according to the loose powder method and “point and shoot” technique. Data quality control was performed by analyzing the reference fertilizer samples and certified and reference soil samples. The results revealed that the determined contents of Cd, Mn, and Th were relatively higher in the single-component fertilizers, while the contents of As, Cr, Fe, Ni, Si, Sr, Zn, Zr, Y, and U were relatively higher in the complex fertilizers. Due to the higher LODs of Co and Pb (3 mg/kg) and Mo (2 mg/kg), the pXRF method was not appropriate for the determination of these metals in the analyzed fertilizers. The quantified metal content in the analyzed fertilizers varied as follows: 2.0–8.0 mg As/kg; 11.5–31.3 mg Cd/kg; 29.8–118.5 mg Cr/kg; 7.8–26.3 mg Cu/kg; 16.5–2209 mg Fe/kg; 20.3–5290 mg Mn/kg; 6.2–27.8 mg Ni/kg; 1156–4581 mg Si/kg; 2.0–469.8 mg Sr/kg; 3.0–35.3 mg Th/kg; 2.0–82.8 mg U/kg; 1.4–166 mg Zn/kg; 9.7–15.3 mg Zr/kg; and 16.5–128.0 mg Y/kg. The results indicated that the pXRF method is particularly suitable for measurement and metal detection in complex nitrogen mineral fertilizers with higher amounts of metals, but it is not suitable for the detection and quantification of the lower amounts of As, Zr, Y, Cu, Ni, and Cr in single-component nitrogen fertilizers. Compared to all of the investigated fertilizers, the highest amounts of As, Cr, Cu, Fe, Ni, U, Zn, and Zr were quantified in the NPK 7-20-30 formulation.