After fungal decay experiments chemical characterisation of the wood is often a routine and several methodological approaches are available. In this study, we tested if simultaneous thermal analysis (STA) is a valid alternative to traditional wet chemical methods since STA allows significantly smaller sample size and faster analysis. Three model fungi including the brown rot fungi Rhodonia placenta and Gloeophyllum trabeum and the white rot fungus Trametes versicolor were employed in the study using Norway spruce as substrate. The experiment was harvested after 10, 20 and 52 weeks. At each harvest interval, aliquots of the material were characterized by STA and wet chemical methods. The results validated that STA can be effectively used to estimate cell wall composition of brown rot depolymerised wood. However, STA slightly overestimated cellulose at brown rot decay above 50%. The method was not verified for simultaneous white rot because STA only estimated hemicellulose correctly compared to the wet chemical method. Hence, STA is considered suitable for brown rot fungi below 50% mass loss but not for simultaneous white rot because STA did not estimate cellulose and lignin correctly.