Abstract Wood meal was submitted to kraft cooking in a small-scale flow-through reactor and the structural changes of lignin have been investigated. The rate determining steps in kraft cooking were in focus. Based on two-dimensional nuclear magnetic resonance (2D-NMR) measurements on lignin fractions extracted at different cooking times from the black liquor, it was observed that the main lignin reactions occur within 10–20 min and thus the kinetics of the chemical reaction cannot be the rate-determining step. On the other hand, the molecular weight (MW) of lignin is shifted towards larger fragments in the course of cooking time but the MW decreases with increasing ionic strength. Obviously, the kinetics of the delignification are strongly dependent on solubility and/or mass transport at the cell wall level. At chip size level, the mass transport of cooking chemicals into the wood chip may influence the overall kinetics in the initial part of the cooking. At longer cooking times the concentration of chemicals becomes sufficiently high in the wood chips, and the delignification is progressively governed by solubility and/or mass transport of lignin molecules occurring at the cell wall level.