A methodology was developed for the calibration of carbonate matrices using portable X-ray fluorescence equipment (pXRF), which involved the analysis of 11 solid mixtures prepared with certified reference material PACS-3 and an analytical CaCO3 reagent as diluent. Of the 31 elements detected in the solid mixtures, significant linear regressions (P < 0.001) were obtained for 20 of them (Al, As, Ca, Cu, Fe, Hg, Mn, Mo, P, Pb, S, Si, Sr, Ti, Zn, K, V, Rb, Y, Zr). The first 17 yielded the best fit with a correlation coefficient of >0.90. The elements Rb, Zr and Y could have been reliably measured with the pXRF if their certified concentrations in PACS-3 were reported, given that they showed a highly significant correlation (P < 0.001) with their respective percentages in the solid mixture. The main advantages of the calibration method include (1) its low cost resulting from the use of a single certified reference material, (2) an excellent linear fit (R = 0.924 to 1.000, for Mo and Zn, respectively), obtained in the calibration, and (3) the possibility of combination with other calibration techniques reported in the literature. The new calibration technique was used to determine the concentrations of major and trace elements in carbonate sediments of the Yucatan continental shelf. Finally, the spatial sampling resolution of the pXRF, equivalent to the diameter of the X-ray beam, was determined to be 6.25 ± 0.55 mm. This methodology allows rapid analysis, low cost and shows an excellent application to carbonate matrices.