The conservation of wooden cultural heritage from wet sites is challenging. Depending on its degree of degradation, waterlogged archaeological wood will collapse, shrink and distort upon drying. Besides damage in the surface, the structure itself is damaged leading to destabilisation or a completely damaged object. Conservation measures are a prerequisite for the preservation of the find material. The various conservation methods available can prevent this damage, but in some cases only up to a certain degree. The evaluation of the conservation methods is usually limited to the surface of the object. Invasive methods, such as the examination of core holes under the microscope, provide information about the structure of the sample, but only a small area of the sample can be examined with preparative effort. In this study, we aimed to analyse both the three-dimensional changes and the inner structure of the conserved wooden samples. Therefore, we used structured-light 3D-Scans before and after conservation and micro-computed tomography (µCT) after conservation. The samples were conserved with some of the most common conservation methods: besides the alcohol-ether-resin method, the conservation methods by impregnation with melamin-formaldeyde (Kauramin 800), lactitol/trehalose, saccharose and silicone oil were investigated. In addition, different polyethylene glycol (PEG) treatments with subsequent freeze-drying were also investigated: one-stage with PEG 2000, two-stage with PEG 400 and PEG 4000 and three-stage with PEG 400, PEG 1500 and PEG 4000. On the basis of the data we analysed and classified the damage patterns in the conserved samples according to a catalogue. These were shrinkage, collapse and cracks. The best results were obtained by the conservation methods using PEG and freeze-drying, alcohol-ether-resin method as well as Kauramin 800. This evaluation showed the respective disadvantages of the individual conservation methods. These damages provide indications for the further development of the methods.