Wood has been extensively used as a material for different applications over the years, therefore the understanding of different degradation processes in various environments is of great importance. In this study, the infrared spectroscopy, X-ray diffraction and chemometric methods were used to evaluate and compare the structure of archaeological and artificially degraded oak wood. The results clearly show that modifications in the structure of archaeological wood are related to the position of the material in the log (sapwood and heartwood), thus the extent of wood degradation. To identify the possible factors influencing these effects, the control wood samples were exposed to artificial white rot biodegradation with Coriolus (Trametes) versicolor and to alkali treatment (with NaOH solution). Due to the structural similarities between biodegraded wood and control or archaeological samples, this type of decay is likely to occur during natural ageing along with degradation produced by other environmental factors. Further, no real similarity was identified between the alkali treated wood and archaeological samples, indicating that such degradation does not affect wood under natural conditions. Display omitted •Archaeological waterlogged and artificially degraded wood samples were analysed.•FT-IR spectroscopy, X-ray diffraction and chemometric methods were used to evaluate wood structure.•Structural modification of archaeological wood was related to its initial structure.•Differences between sapwood and heartwood of archaeological samples were observed.•Excessive depletion of carbohydrates was observed for sapwood archaeological sample.