The purification of biofuels becomes a challenging issue because of the harmfulness of remaining phenolic molecules for human health and engines. To this end, protonic Y zeolites with different Si/Al ratios were explored as effective adsorbent materials to remove phenol from isooctane solution by using a dual experimental/computational strategy. Phenol was selectively removed from isooctane over HY and USY zeolites with a maximal adsorption capacity of 2.2 mmol·g–1, which corresponds to 3–4 phenol molecules per zeolitic supercage. The adsorption equilibrium was reached faster over dealuminated zeolites, due to the presence of large pores at the expense of microporosity as well as a low density of acidic sites. We further evidence that the presence of acid sites limits the regeneration capacity since phenol was strongly adsorbed on both Brønsted and Lewis acid sites. USY zeolite with the highest Si/Al ratio presents the best regeneration capacity since it has the lower aluminum loading. A fundamental understanding of these performances was obtained by coupling characterization (infrared spectroscopy, breakthrough curves, and desorption experiments) and modeling tools (Grand Canonical Monte Carlo and Density Functional Theory).