Heavy crude oil processing leads the way in current refining. These crudes yield larger amounts of distillable heavy fractions such as vacuum gas oil (VGO). VGO must be treated in at least two refining units: a hydrotreating unit where sulfur, nitrogen, and other heteroatoms are removed, and a hydrocracking unit where suitable fuels are obtained. Removal of heteroatoms during hydrotreating, particularly, nitrogen, dictates the efficiency of hydrocracking. In the first part of this work, the nature of refractory nitrogen-containing compounds on the performance of a hydrotreating catalyst was evaluated. To achieve this goal, both a VGO and its hydrotreated counterpart were studied using electrospray ionization with Fourier transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR-MS). Weakly basic N-containing compounds, namely, heavy pyrrolic-like compounds and their partially hydrogenated derivatives, were found to be the most refractory to hydrotreating. These compounds are weakly basic compared to most nitrogen compounds present in VGO. Considering this finding, the second part of the work was devoted to assessing the effect of pyrroles on the reactivity of phenanthrene over a Ni-MoS2/Y-zeolite-alumina two-stage hydrocracking catalyst. Tests were carried out in a fixed-bed reactor using mixtures of carbazole and tetrahydrocarbazole. Results showed that these compounds can affect the catalytic performance of Ni-MoS2/Y-zeolite-alumina by reducing its activity and inhibiting its selectivity to hydrocracking products. These findings draw attention to the possible role of weakly basic nitrogen compounds in the catalytic performance of materials employed for two-stage hydrocracking units.