Biofuels may contain phenolic molecules, which are toxic for humans and can significantly affect engine performance. In this context, amorphous silica surfaces are attractive since they have the potential to separate the harmful molecules from the biofuel constituents through a selective adsorption process. Here, density functional theory is employed to describe the different adsorption modes of toluene and phenol, chosen as model molecules, on amorphous silica surfaces with various silanol densities. It is found that surfaces with densities of 2.0, 3.3, and 4.6 OH/nm 2 are optimal to trap phenol, with certain configurations attaining an adsorption energy of more than 100 kJ/mol. These trends remain similar at 300 K as shown by our molecular dynamics simulations, although the interaction energy between the molecules and the surface is reduced due to the temperature.