This study explores deep eutectic solvents (DESs) as potential alternatives to dimethylformamide (DMF) for extractive desulfurization of gas oil and marine fuel oil. A series of DESs, based on choline chloride (ChCl) and tetrabutylammonium bromide (TBAB), were evaluated using straight-run gas oil (SRGO) and compared to DMF. The influence of an oxidation pre-treatment and water content was also investigated, and the most efficient systems were further applied to marine fuel oil. Firstly, oxidation was found to be essential to enhance sulfur removal by improving the extractability of sulfone compounds. The results show that DES formulation strongly affects desulfurization performance, with TBAB-based DESs achieving efficiencies comparable to DMF (~80% desulfurization rate) and outperforming ChCl-based systems. In ChCl-based DESs, a moderate water content (~10 wt%) improved performance, whereas higher amounts disrupted the hydrogen-bond network, as evidenced by Fourier-transform infrared spectroscopy, leading to a decreased efficiency. When applied to marine fuel oil, similar trends were observed, although lower desulfurization levels were obtained due to the complexity of the feed, and a solvent-to-fuel ratio of 5:1 was required for proper phase separation. Fourier transform mass spectrometry analyses highlighted the persistence of refractory sulfur species, emphasizing the need for tailored solvent design. Overall, DESs represent promising and adaptable alternatives for desulfurization processes.