A way to improve hydrotreatment processes is to enhance the intrinsic activity of Ni or Co promoted MoS2 catalysts that are commonly used in such reactions. The aim of this work was to investigate the impact of the presence of Pluronic® P123 as a structuring agent during the synthesis of Ni promoted MoS2 catalysts (named NiMoS) in water at room temperature. A series of analyses, i.e., X-ray diffraction (XRD), chemical analysis, inductively coupled plasma mass spectrometry (ICP-MS), nitrogen adsorption-desorption isotherms, transmission electron microscopy (TEM) and X-ray photoelectron spectroscopy (XPS), helped in characterizing the NiMoS-P123 and NiMoS catalysts, the latter being prepared in the absence of polymer. Both compounds contained MoS2 phase (~85 atomic% considering Mo atoms), a similar amount of mixed Ni-Mo-S phase (40–50% considering Ni) and some amount of NiS and Ni-oxidized impurity phases. The main differences between the two catalysts were a much larger specific surface area (126 m2·g−1 instead of 31 m²·g−1) and a better dispersion of the active phase as shown by the lower slab stacking (2.7 instead of 4.8) for NiMoS-P123, and the presence of C in NiMoS-P123 (9.4 wt.% instead of 0.6 wt.%), indicating an incomplete decomposition of the polymer during thermal treatment. Thanks to its larger specific surface area and lower slab stacking and therefore modification of active Mo site properties, the compound prepared in the presence of Pluronic® P123 exhibits a strong increase of the catalytic activity expressed per Mo atom for the transformation of 3-methylthiophene. Such improvement in catalytic activity was not observed for the transformation of benzothiophene likely due to poisonous residual carbon which results from the presence of Pluronic® P123 during the synthesis.