The modification of the lignin structure of an eucalyptus feedstock during alkaline delignification by kraft, soda-AQ, and soda-O2 cooking processes has been investigated by different analytical techniques (size exclusion chromatography (SEC), pyrolysis gas chromatography–mass spectroscopy (Py-GC/MS), 1H–13C two-dimensional nuclear magnetic resonance (2D-NMR), and 31P NMR). The characteristics of the lignins were compared at different pulp kappa levels, and with the native lignin isolated from the wood. The structural differences between the kraft, soda-AQ, and soda-O2 residual lignins were more significant at earlier pulping stages. At the final stages, all the lignin characteristics were similar, with the exception of their phenolic content. Strong differences between lignins from pulps and cooking liquors were observed, including enrichment in guaiacyl units in pulp residual lignin and enrichment in syringyl units in black liquor lignin. A comparison of the alkaline cookings indicate that soda-O2 process produced higher lignin degradation and provided promising results as pretreatment for the deconstruction of eucalyptus feedstocks for subsequent use in lignocellulose biorefineries.