The removal of sulfur compounds, particularly thiophene derivatives, from oil is crucial due to concerns about environmental issues. Therefore, the deep desulfurization of transportation fuels is currently an urgent problem, and numerous attempts have been made in this direction. Membrane-based desulfurization can be a good alternative to the traditional hydrodesulfurization method, which has several limitations. In this work, the use of membranes containing a metal-organic framework, MOF-5, doped with transition metals (Ag, Cu, Ni), in the adsorptive desulfurization process was studied. The efficiency of membranes was evaluated based on selective removal of thiophene and dibenzothiophene from model oil. Characterization techniques, including scanning electron microscopic (SEM), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), and thermogravimetric analysis (TGA), confirmed the successful synthesis and incorporation of metal-organic frameworks (MOFs) into mixed matrix membranes (MMMs). Desulfurization experiments showed that MOF-5/Ag exhibited the highest thiophene adsorption efficiency (86.8%), outperforming MOF-5/Cu and MOF-5/Ni. The enhanced performance is attributed to the strong interaction between silver and sulfur. These findings demonstrate the potential of MOF-based MMMs for efficient and selective desulfurization, offering a viable alternative to traditional hydrodesulfurization (HDS) methods.