Considerable health and climate benefits arising from the use of low-sulfur fuels has propelled the research on desulfurization of fossil fuels. Ideal fuels are urgently needed and are expected to be ultra-low in sulfur (10–15 ppm), with no greater than 50 ppm sulfur content. Although several sulfur removal techniques are available in refineries and petrochemical units, their high operational costs, complex operational needs, low efficiencies, and higher environmental risks render them unviable and challenging to implement. In recent years, mesoporous silica-based materials have emerged as promising desulfurizing agents, owing to their high porosity, high surface area, and easier functionalization compared to conventional materials. In this review, we report on recent progress in the synthesis and chemistry of new functionalized mesoporous silica materials aiming to lower the sulfur content of fuels. Additionally, we discuss the role of special active sites in these sorbent materials and investigate the formulations capable of encapsulating and trapping the sulfur-based molecules, which are challenging to remove due to their complexity, for example the species present in JP-8 jet fuels.