Zeolite Y is a widely used adsorbent due to its high surface area and well-defined pore structure, making it suitable for removing organic contaminants from fuel streams. In this study, the adsorption capacity of zeolite Y was enhanced by ion exchange with nickel (Ni2+) cations, and the resulting Ni-NaY material was characterized using X-ray diffraction, thermogravimetric analysis, and X-ray fluorescence spectroscopy. The chemical stability of the modified zeolite was investigated in the presence of sulfur-containing compounds such as 1,2-Ethanedithiol (1,2-ED), 1-Butanethiol (1-BT), 1-Octanethiol (1-OT), and Cyclohexanethiol (CT) dissolved in n-hexane to simulate model diesel. The results revealed that 1-BT had the highest potential to decompose the Ni-NaY adsorbent, removing a significant amount of Ni and thereby reducing the zeolite’s adsorption capacity. Elemental analysis confirmed that the extent of framework decomposition correlated with the nature of the organic linker. Key factors affecting the adsorbent’s degradation included the polarity of the solvent, the electronic structure and polarity of functional groups, the size and flexibility of organic molecules relative to zeolite pore dimensions (steric hindrance), and the ability to form strong S–M (sulfur–metal) interactions. These findings provide new insights into the degradation pathways of transition-metal-exchanged zeolites in sulfur-rich fuel environments and highlight critical considerations for the design of more durable adsorbents.

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