Widespread use of per- and polyfluoroalkyl substances (PFAS) poses significant ecological and health risks due to their non-degradability in the environment and consequent bioaccumulation in humans. In this work, we carried out a systematic computational study to unravel the effect of perfluorinated carbon chain length and the type of acid head group on the adsorption mechanism of PFAS from water. We considered the adsorption of perfluoroalkyl carboxylic acids (PFCA) and perfluoroalkyl sulfonic acids (PFSA) with chain lengths of three to eight perfluorinated carbons in hydrophobic all-silica zeolite Beta. Molecular dynamics (MD) simulations coupled with enhanced sampling calculations showed that adsorption free energies of both PFCA and PFSA decreased with increasing number of perfluorinated carbons. Calculated free energies further showed that PFCA and PFSA, which are anions in water, must overcome substantially large interfacial energy barriers to be adsorbed in hydrophobic pores. Subsequent ab initio MD simulations revealed that PFCA and PFSA gain a proton at the water–zeolite interface and are eventually adsorbed in neutral form. Breakdown of guest–host interaction energies into hydrophobic and polar components showed that hydrophobic interactions dominate PFCA adsorption whereas polar interactions are dominant in PFSA adsorption. This is due to sulfonic acid giving rise to stronger electrostatic interactions and the rearrangement of the electron density distribution in the perfluorinated carbon chain, which render the hydrophobic interactions relatively weaker. Our study reveals that a combination of adsorbents that provide optimized hydrophobic and polar interactions should be used for the capture of diverse PFAS from water.