In order to examine the influence of type of metal precursor on the hydrodesulfurization (HDS) activity of synthetized samples, a series of ternary Ni–Mo–W catalysts supported on a natural Mexican zeolite (clinoptilolite) were prepared by sequential wet impregnation of the zeolite support with different thiosalts of W and Mo, and Ni(NO3)2·6H2O. The synthetized samples were characterized by N2 adsorption–desorption isotherms at −196 °C, X-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive X-ray analysis (EDX/SEM), high-resolution transmission electron microscopy (HRTEM) and X-ray photoelectron spectroscopy (XPS) techniques. The catalysts activity was evaluated in the HDS of dibenzothiophene (DBT) reaction performed in a batch reactor at 350 °C and 3.1 MPa of total hydrogen pressure. The activity tests demonstrated that the best catalyst was the NiMoW-H/zeo sample synthesized from ammonium thiosalts. The use of tetraalkylammonium thiometalates as metal precursors led to the decrease in the HDS activity. The most active catalyst in the HDS of DBT reaction showed the largest density of active phases on the support surface determined from HRTEM measurements.