Dietary supplements may contain heavy metals with the property of bioaccumulation in humans. The aim of this research was to validate and apply two analytical methods to determine Pb, As, Cr, and Hg in dietary supplements by Total Reflection X-ray Fluorescence Spectroscopy (TXRF). Methods validation was conducted through a multivariate analysis using a central composite design (CCD) and a desirability function. Critical values for each study variable were established. The TXRF_DS_1 method was proposed for Pb, As, and Cr determinations, while the TXRF_DS_2 was established for Hg analysis. The digestion method with an acid mixture (HNO3 + HCl + H2O2) was used to break down the organic material of dietary supplements. A solution of 10 μg L−1 Ga was used as an internal standard. Excellent analytical performance was obtained as LODs of 0.59, 0.41, 0.57, and 0.75 μg L−1 and LOQs of 1.95, 1.35, 1.90, and 2.50 μgL −1 for Pb, As, Cr, and Hg, respectively. Calibration curves showed a good linearity for all elements (R2>0.999). Excellent accuracy and precision in measurements (% RSD) was achieved. The real and spiked samples analysis demonstrated the applicability of the TXRF technique (percentage recovery 91–108%). Besides, two samples were analyzed in a comparison study between the TXRF_DS_1 method and the ICP-OES method. The results obtained showed good agreement between both techniques. The TXRF technique allows the analysis of toxic heavy metals in dietary supplements, which are marketed in a wide variety of presentations.