A series of silica-based aerogels comprising novel bifunctional chelating ligands was prepared. To produce target aerogels, two aminosilanes, namely (3-aminopropyl)trimethoxysilane (APTMS) and N-(2-aminoethyl)-3-aminopropyltrimethoxysilane (AEAPTMS), were acylated by natural amino acids ((S)-(+)-2-phenylglycine or L-phenylalanine), followed by gelation and supercritical drying (SCD). Lithium tetrachloropalladate was used as the metal ion source to prepare strong complexes of Pd2+ with amino acids covalently bonded to a silica matrix. Aerogels bearing chelate complexes retain the Pd2+ oxidation state after supercritical drying in CO2, but the Pd ion is reduced to Pd metal after SCD in isopropanol. Depending on the structure of amino complexes, Pd-containing aerogels showed catalytic activity and selectivity in the hydrogenation reactions of C=C, C≡C and C=O bonds.