Dissolving pulps are technically produced by prehydrolysis kraft, one-stage or two-stage acid sulfite pulping. Like other pulping methods, the delignification process is incomplete and bleaching is required for complete lignin removal. Here, we explored the molecular aspects of lignin recalcitrance during the pulping, in order to gain insights that could inform future pulping efforts. For this purpose, we adopted a protocol for the controlled fractionation of pulp into soluble fractions that could be analyzed by spectroscopic methods including size exclusion chromatography (SEC) and 2D NMR methods. In addition, lignosulfonates (i.e. technical lignin) was analysed as a reference to gain insights on the structural basis for dissolution. Overall, the results identify a sequence of reactions responsible for the dissolution of lignin. In the first stage, the sulfonation of lignin begins and occurs at the alpha-carbon of beta-O-4 and beta-5 sub-structures. In the second stage the cleavage of lignin carbohydrate bonds (LCC) of benzyl ether, gamma ester and phenylglycosides types, all of which were detected in the residual lignin of the earlier phases, occurs and enhances lignin dissolution. Finally, condensation reactions of benzylic cations with activated positions on aromatic ring were detected in lignosulfonates. This suggest that a competing reaction mode to the sulfonation at C-alpha position in lignin was occurring at prolonged pulping conditions, here considered to be unproductive.