AbstractTwo‐dimensional layered double hydroxides (LDHs) are ideal candidates for a large number of (bio)catalytic applications due to their flexible composition and easy to tailor properties. Functionality can be achieved by intercalation of amino acids (as the basic units of peptides and proteins). To gain insight on the functionality, we apply resonant inelastic soft x‐ray scattering and near edge x‐ray absorption fine structure spectroscopy to CaFe LDH in its pristine form as well as intercalated with the amino acids proline and cysteine to probe the electronic structure and its changes upon intercalation. We observe the activation of pristine LDH defect states by soft x‐rays and their passivation by the intercalated molecules. The nitrogen at the amino amino is found to form C=NH+ bonds and thus generating positive charge at the amino group, moving it away from the positively charged LDH layers. The carboxyl group in cysteine is deprotonated and thus in zwitterionic state after intercalation. This negative charge is used to compensate the positive layer charge. For intercalated proline the spectral signature of a protonated carboxyl group is observed, however, we find orbital overlap to defects at the layer surfaces indicating strong interaction with the carboxyl groups.