A new laboratory reactor to perform in situ studies of structural changes in wood during soda pulping using synchrotron X-ray tomography is presented. The reactor is of recirculation type to provide stable reaction conditions and mimic the industrial situation. Experiments have been performed using this reactor in situ at a synchrotron microtomography beamline to provide sequences of 3D images from which measurement of wood cell wall thickness have been possible for the first time. The results showed that the cell wall thickness increased significantly in the early stage of pulping (<10 min), which is due to the transportation of cooking chemicals through the tracheids, resin channels and pits into the cell wall, which is swollen with the increased pH. Subsequently, the cell wall thickness reduces over the processing time up to 60 min with a high rate, which is inferred to be due to the dissolution and transport of lignin and hemicellulose from the secondary walls, allowing for better transportation of active chemicals deep through the cell wall layers. After 60 min processing, the cell wall thickness reduction rate reduced, as dissolution of lignin and hemicelluloses from the cell walls ceased, while the remaining dissolution occurs mainly at the middle lamella.