Core level spectroscopy is a powerful tool to achieve a fine understanding of both the electronic and the geometric structure of heterogeneous catalysts. The present work shows use of photon-in/photon-out spectroscopy to investigate the structures of hydrodesulfurization catalysts actives sites. Despite countless studies carried out to understand the working phase of this class of catalyst, the exact localization of the promoter (cobalt) remains an open question for the “real hydrodesulfurization (HDS) catalyst”. The difficulty comes from the segregation of cobalt in different phases during the catalyst activation step. Consequently, most collected spectroscopic signal of cobalt involved in the catalyst, will corresponds to a weighted average of the contributions arising from all cobalt centers (active phase, nonactive sulfide phase, and the remaining cobalt oxide phase). To overcome this problem, for the first time in situ Co K-edge HERFD-XAS is used to discriminate between oxide (CoII–O) and sulfide (CoII–S) phases arising during HDS catalyst activation, allowing the localization of cobalt in the active phase of the catalysts. We find that Co is localized at S-edges of the MoS2 layers. Furthermore, in situ Co K-edge 1s2p RIXS of the sulfided catalyst shows excitations to bandlike unoccupied states revealing the metallic nature of cobalt in these structures. A new XPS fitting procedure, considering the exact electronic structure of the active phase is proposed bringing us to reconsider earlier Co-promotion rate published in the literature for a better correlation with the catalytic activity.