Unsupported Ni-Mo sulfides have been hydrothermally synthesized and purified by HCl leaching to remove Ni sulfides. Unblocking of active sites by leaching significantly increases the catalytic activity for dibenzothiophene hydrodesulfurization. The site-specific rates of both direct (hydrogenolytic) and hydrogenative desulfurization routes on these active sites that consist of coordinatively unsaturated Ni and sulfhydryl groups were identical for all unsupported sulfides. The hydrogenative desulfurization rates were more than an order of magnitude higher on unsupported Ni-Mo sulfides than on Al2O3-supported catalysts, while they were similar for the direct (hydrogenolytic) desulfurization. The higher activity is concluded to be caused by the lower average electronegativity, i.e., higher base strength and polarity, of Ni-Mo sulfides in the absence of the alumina support and the modified adsorption of reactants enabled by multilayer stacking. Beyond the specific catalytic reaction, the synthesis strategy points to promising scalable routes to sulfide materials broadly applied in hydrogenation and hydrotreating.