The purification of second-generation biofuels is becoming an urgent issue due to the toxicity of the combustion products of residual phenol in these biofuels. The use of solid sorbents such as zeolites appears as a promising solution for ensuring the selective sorption of phenol towards aromatics (the main components of biofuel). In the present work, we have adopted a bottom-up approach for removing phenol from a synthetic biofuel feed containing isooctane, 1 wt.% phenol, 1 wt.% n-nonane and 40 wt.% toluene, using faujasitetype Y zeolites with Si/Al ratio = 2.5. The adsorption modes of the molecules involved have been assessed by comparing theoretical and experimental infrared spectra. In addition, coupling molecular modeling with breakthrough curves has revealed the important role of protons embedded in zeolites for the selective removal of phenol.