Downstream processing of biochemical products strongly depends on the interaction between biomolecules and material surfaces that can be influenced greatly by the pH level. In this study, the influence of the pH value on the adsorption of the amino acids glycine, alanine, and lysine in MFI-type zeolite was investigated using density functional theory (DFT) and microcalorimetric experiments. Different pH values were modeled by varying the amino acids protonation states. The investigated protonation states exhibit two different adsorption motifs in the pores, with the neutral α-C-amino group motifs being significantly less stable than the protonated ones. In the case of neutral glycine and alanine, the adsorption energy is insufficient to overcome the adsorption of the four water molecules usually present in the pores. This result explains the pH-dependent adsorption behavior that has also been observed experimentally and provides an avenue for designing efficient adsorption processes.