Adsorptive desulfurization of sulfur compounds in transportation fuels, such as benzothiophenes from gasoline and jet fuels and dibenzothiophenes from diesel, can be inhibited by diffusion limitations in porous materials as well as the presence of aromatic hydrocarbons. In this study we demonstrate that adsorptive desulfurization using bimetal-exchanged mesoporous Y zeolites can overcome these challenges without sacrificing high sulfur adsorption capacity. The mesopores shorten the diffusion path length toward the internal active sites of the zeolite, while the metals (in this study Ce and Cu), not only create relatively stronger bonds, but also multiple adsorption configurations. The bimetallic mesoporous Y zeolites were prepared using a templated top-down approach, followed by the introduction of the metals, Cu and Ce, via ion-exchange. The ability of each zeolite to remove sulfur compounds is demonstrated by fixed-bed experiments. Model fuels were prepared using benzothiophene and dibenzothiophene in octane, benzene and naphthalene. The adsorption mechanisms of benzothiophene and dibenzothiophene were further studied, at the molecular level, using in-situ Diffuse Reflectance Infrared Fourier Transform Spectra (DRIFTS). Our results indicate that the metals display high affinity for the aforementioned sulfur compounds, via either pi-complexation or sigma-bond interaction. Specifically, Ce-exchanged Y zeolites exhibit multiple adsorption modes, as they can adsorb the sulfur compounds via the both configurations. Furthermore, the mesoporosity in Y zeolites enable the adsorption of dibenzothiophene with a diffusion coefficient of 4.5x greater than the parent Y zeolite. In conclusion, bimetallic mesoporous Y zeolites exhibited DBT capacity of almost 50 mL/g, five times more than parent Y, due to both improved mass transfer and high adsorption energy.