Residue upgrading processes are very important for the production of distillates and low sulfur fuel oils. Among those, fixed bed technologies are very efficient for deep desulfurization of petroleum residue heavy oils, even for highly asphaltenic feeds. This work analyzes the effects of the operating conditions on the evolution of asphaltenes and on their inhibition effect during the hydrodesulfurization reactions. Residue hydrotreating experiments were performed on a pilot plant and asphaltene fractions were investigated using size exclusion chromatography (SEC), 13 C nuclear magnetic resonance (NMR), liquid chromatography, and elemental analyses. Besides the overall decrease in asphaltenes yield, significant changes in the average structure of the asphaltenes were also observed.