This investigation focuses on getting a further understanding of the wood degradation processes based on results obtained by chemical analysis (combining mid-infrared spectroscopy and analytical pyrolysis) of waterlogged woods recovered from an acidic marsh sediment during an archaeological excavation at the O Areal archaeological site (Vigo, NW Spain). The woods consist of eight oak (Quercus sp.) and two cherry (Prunus sp.) remains that were radiocarbon dated between 6100 and 5990 cal BC. The results indicate clear changes in the wood’s chemical composition related to the degradation of the polysaccharide and lignin compounds. The chemical changes are attributed to various degradation processes, including, (i) hydrolysis of polysaccharides, (ii) partial depolymerization of lignin as well as polysaccharides, and (iii) partial oxidation of the lignin. Furthermore, contrasting the pyrolysis data with mid-infrared results enabled to connect specific mid-infrared signals with depolymerization and oxidation of the lignocellulosic components in the studied waterlogged wood material. Our findings point out that an accurate interpretation of waterlogged wood chemical degradation requires considerations beyond the commonly stated depletion of wood polysaccharide content. Finally, this study demonstrates that integrating FTIR-ATR spectroscopy and analytical pyrolysis provides a comprehensive and detailed analysis of chemical changes during wood degradation. Such an outcome may be crucial for conservators seeking to identify and address the vulnerabilities of waterlogged ancient wood exposed to specific burial conditions like highly acidic environments.