Amino sugars in soils have been used as markers of microbial necromass and to determine the relative contribution of bacterial and fungal residues to soil organic matter. However, little is known about the dynamics of amino sugars in soil. This is partly because of a lack of adequate techniques to determine ‘turnover rates’ of amino sugars in soil. We conducted an incubation experiment where 13C-labeled organic substrates of different quality were added to a sandy soil. The objectives were to evaluate the applicability of compound-specific stable isotope analysis via gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS) for the determination of 13C amino sugars and to demonstrate amino sugar dynamics in soil. We found total analytical errors between 0.8 and 2.6‰ for the δ13C-values of the soil amino sugars as a result of the required δ13C-corrections for isotopic alterations due to derivatization, isotopic fractionation and analytical conditions. Furthermore, the δ13C-values of internal standards in samples determined via GC-C-IRMS deviated considerably from the δ13C-values of the pure compounds determined via elemental analyzer IRMS (with a variation of 9 to 10‰ between the first and third quartile among all samples). This questions the applicability of GC-C-IRMS for soil amino sugar analysis. Liquid chromatography-combustion-IRMS (LC-C-IRMS) might be a promising alternative since derivatization, one of the main sources of error when using GC-C-IRMS, is eliminated from the procedure. The high 13C-enrichment of the substrate allowed for the detection of very high 13C-labels in soil amino sugars after 1 week of incubation, while no significant differences in amino sugar concentrations over time and across treatments were observed. This suggests steady-state conditions upon substrate addition, i.e. amino sugar formation equalled amino sugar decomposition. Furthermore, higher quality substrates seemed to favor the production of fungal-derived amino sugars. Copyright © 2009 John Wiley & Sons, Ltd.