The oxidative desulfurization (ODS) of heavy fuel oil (HFO) offers a promising solution for desulfurizing marine fuels under mild conditions, in line with current environmental regulations. While most studies focus on model or light fuels, explaining deactivation through leaching or sulfone adsorption, the deactivation mechanisms of catalysts in HFO remain poorly understood. In this work, Mo-based catalysts supported on alumina were extensively characterized before and after catalytic reactions, and regeneration through air calcination was considered. Techniques such as XRD, Raman spectroscopy, XRF, and TGA, alongside catalytic testing with H2O2 as an oxidant, revealed that Mo surface speciation significantly impacted both activity and deactivation. Contrary to well-dispersed polymolybdates, crystalline MoO3 induced low activity and hindered regeneration. No leaching of the active phase was demonstrated during the reaction. Sulfone adsorption had minimal impact on deactivation, while non-sulphur compounds appeared to be the key contributors. Regeneration outcomes were found to be molybdenum content-dependent: 10Mo/Al recovered its activity, while 20Mo/Al formed inactive phases, like Al2(MoO4)3. Using an organic oxidant (tBHP) during ODS influenced the regeneration, as it prevented Al2(MoO4)3 formation and redispersed crystalline MoO3, enhancing performance. These findings advance understanding of catalyst deactivation and suggest strategies to extend catalyst life in the ODS of HFO.