The kraft process is the main process used for the production of chemical pulps. In this process, an efficient delignification is achieved, yielding bleachable grade pulps. In recent years, there has been interest in valorization of the dissolved lignins, prompted by the development of technically feasible processes to retrieve it from the black liquor. However, the structural-, functional-, and size-related heterogeneities of lignin present both analytical challenges and challenges in developing new applications. Hence, refining of the crude product is essential. Herein, advanced NMR characterization (13C NMR, APT/DEPT NMR, 31P NMR, HSQC, HMBC, HSQC-TOCSY) was applied to profile the detailed molecular structures of refined kraft lignins and unravel mechanistic insights on important lignin reactions during kraft pulping. From this structural analysis of the lignins, a model oligomer was synthesized and analyzed to provide support to the effect that a retro-aldol reaction in combination with radical recombination reactions play a significant role in the formation of the reconstituted fraction of kraft lignin. In this regard, a new type of linkage accounting for approximately 10% of the interunits in kraft lignin is reported.