Research on new conservation treatments for historical wood requires considerable amounts of appropriate wood material, which is hard to acquire. Thus, we produced biologically and chemically degraded model wood that could be used as a representative material in future research on consolidating agents. Using chemical composition determinations, we found that fungal decay targeted mainly polysaccharides, while alkaline treatment mostly reduced hemicelluloses and lignin content. X-ray and neutron scattering showed that all decayed samples had increased disorder in microfibril alignment and larger elementary fibril cross-sections, and alkaline-treated samples had much larger elementary fibril spacing compared to those decayed by fungi. These nanoscale and chemical differences correlate with physical property changes. For example, decreased cellulose crystallinity and increased disorder of the microfibrils in degraded cell walls likely contribute to the lower elastic moduli measured for these cell walls. The obtained data improves understanding of how degradation alters wood structures and properties across length scales and will be valuable for future studies focusing on archeological wood. Moreover, it leads to the conclusion that it is more appropriate to develop treatments that consider not only spatial variability and degree of wood degradation but also the corresponding molecular and nanoscale changes in the cell walls.