Nanoparticle engineering for catalytic applications requires both a synthesis technique for the production of well-defined nanoparticles and measurements of their catalytic performance. In this paper, we present a new approach to rationally engineering highly active Ni-Mo-S nanoparticle catalysts for hydrodesulfurization (HDS), i.e., the removal of sulfur from fossil fuels. Nanoparticle catalysts are synthesized by the sputtering of a MoNi metal target in a reactive atmosphere of Ar and HS followed by the gas aggregation of the sputtered material into nanoparticles. The nanoparticles are filtered by a quadrupole mass filter and subsequently deposited on a planar substrate, such as a grid for electron microscopy or a microreactor. By varying the mass of the deposited nanoparticles, it is demonstrated that the Ni-Mo-S nanoparticles can be tuned into fullerene-like particles, flat-lying platelets, and upright-oriented platelets. The nanoparticle morphologies provide different abundances of Ni-Mo-S edge sites, which are commonly considered the catalytically important sites. Using a microreactor system, we assess the catalytic activity of the Ni-Mo-S nanoparticles for the HDS of dibenzothiophene. The measurements show that platelets are twice as active as the fullerene-like particles, demonstrating that the Ni-Mo-S edges are more active than basal planes for the HDS. Furthermore, the upright-standing orientation of platelets show an activity that is six times higher than the fullerene-like particles, demonstrating the importance of the edge site number and accessibility to reducing, e.g., sterical hindrance for the reacting molecules.