Preparation conditions have a vital effect on the structure of alumina-supported hydrodesulfurization (HDS) catalysts. To explore this effect, we prepared two NiMoS/Al₂O₃ catalyst samples with the same target composition using different chemical sources and characterizing the oxidic NiMo precursors and sulfided and spent catalysts to understand the influence of catalyst structure on performance. The sample prepared from ammonium heptamolybdate and nickel nitrate (sample A) contains Mo in the oxidic precursor predominantly in tetrahedral coordination in the form of crystalline domains, which show low reducibility and strong metal–support interactions. This property influences the sulfidation process such that the sulfidation processes of Ni and Mo occur tendentially separately with a decreased efficiency to form active Ni–Mo–S particles. Moreover, inactive unsupported MoS₂ particles or isolated NiS_x species are formed, which are either washed off during catalytic reaction or aggregated to larger particles as seen in scanning transmission electron microscopy/energy-dispersive X-ray spectroscopy (STEM/EDX). The oxidic precursor of the sample synthesized using nickel carbonate and molybdenum trioxide as metal sources (sample B), however, contains Mo in octahedral coordination and shows higher reducibility of the metal species as well as weaker metal–support interactions than that of sample A; these properties allow an efficient sulfidation of Mo and Ni such that formation of active Ni–Mo–S particles is the main product. Ptychographic X-ray computed tomography (PXCT) and STEM and EDX measurements show that the structure formed during sulfidation is stable under operation conditions. The structural differences explain the HDS activity difference between these two samples and explain why sample B is much active than sample A.