AbstractA set of peptide‐functionalized mesoporous silica particles is synthesized by chemoselective inverse electron‐demand Diels‐Alder (IEDDA) ligation, exploiting the robust and cost‐effective norbornene/tetrazine coupling chemistry. The peptides program the capabilities of the silica particles to specifically complex and host small organic entities. Customized chromatography columns are packed that are tailored to specifically retard the respective compounds, while other substances elute rapidly. Using combinatorial means, the 7‐mer peptides QFFLFFQ, QFFEFFQ, and QFQQSFF have been previously selected as good, medium, and poor binders, respectively, for the photosensitizer 5,10,15,20‐tetrakis(3‐hydroxyphenyl)chlorin (m‐THPC). These sequences are C‐terminally functionalized with 1,2,4,5‐tetrazine (Tz) moieties to enable IEDDA ligation to silica material presenting endo‐ /exo‐norbornene (Nb) moieties to give pyridazine (Pz)‐linkages. The resulting silica‐Pz‐Peptide materials (Sil‐Pz‐X) retain their pore systems and show peptide loadings of up to 0.19 mmol g−1. The capabilities of the different Sil‐Pz‐X materials to bind the photosensitizer are investigated by incubation/elution batch assays, confirming that the peptides define the binding selectivity and capacity in a sequence‐dependent manner. Professional packing of Sil‐Pz‐X results in a set of high‐performance liquid chromatography (HPLC) columns. HPLC elution studies of m‐THPC and a functional relative, Chlorin E6, show a compound‐specific retardation that clearly reflects the complexation properties of the peptides for the respective photosensitizers.