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Amino acids have been detected in carbonaceous chondrites, with abundances and isotopic compositions varying significantly between different meteorites as well as within individual meteorites. In this study, we assessed whether the presence and abundance of Fe-rich phases during parent body alteration can account for observed variations in amino acid concentrations and isotope composition. To test this, we examined the chemical and 13C-isotopic signatures of six amino acids─glycine, β-alanine, α-alanine, 2-aminoisobutyric acid, γ-aminobutyric acid, and isovaline─following experimental exposure to hydrothermal conditions (150 °C, 10 days) in the presence or absence of Fe-bearing materials (Fe, Fe2O3, FeS2). In the absence of Fe-rich materials, glycine and α-alanine rather withstood hydrothermal conditions, consistently with abundances reported for carbonaceous chondrites having experienced various degrees of aqueous alteration. In contrast, upon exposure to similar hydrothermal conditions, the degradation of β-alanine produced a new compound, possibly 3-aminoadipic acid, via the recombination of products of its decarboxylation and deamination, while more than 95% of γ-aminobutyric acid was converted to 2-pyrrolidone through self-cyclization. The presence of Fe-rich materials inhibited the destruction of β-alanine, 2-aminoisobutyric acid, and γ-aminobutyric acid. Fe2O3 promoted the conversion of glycine into aspartic acid, and the resulting organics interacted with Fe2O3, leading to a relatively higher organic content in the residues compared to other Fe-containing materials after the experiments. Oxides in CI chondrites may exhibit variable effects on each amino acid compound during aqueous alteration, potentially explaining the higher β-Alanine/Glycine ratios observed compared with CM chondrites. The slight changes in δ13C values of amino acids upon exposure to hydrothermal conditions, independent of the presence or absence of Fe-rich materials, could not account for the variations observed in the δ13C values of chondritic amino acids. Hence, the δ13C values of amino acids reported in CR and CM chondrites may be inherited from the preaccretion processes.