Although various stages of decomposition of bone collagen have been reported, the molecular breakdown is still not completely understood. By investigating the stable C and N isotopes of individual amino acids, this study sheds light on the biochemical processes of microbial decomposition. Collagen was extracted from sterilized compact bone of modern martens inoculated with a selection of soil bacteria in the order to induce decomposition. Furthermore, this study determined the amino acid composition, overall stable carbon and nitrogen isotope ratios and isotope ratios of the separated individual amino acids of the collagen. For the bulk collagen, the carbon delta -values of the carboxyl groups were measured. This study demonstrates that the delta 15 N-values of the total collagen were increased, while bulk delta 13 C-values were decreased. With respect to the individual amino acids the delta 15 N-values and especially the delta 13 C-values were decreased. This general isotopic shift of the individual amino acids is not related to the modification of their amounts given by the amino acid profiles of experimentally modified collagen. As expected, the carbon isotope ratios of the carboxyl group surmount the overall value. The observed modifications of the amino acid spectra seem to be the result of a selective breakdown of larger amino acids by soil microorganisms. A probable cause could be the stereo-specific repolymerization of peptides which can create insoluble macromolecules during diagenesis.