We have studied the structural modifications of lignins from sisal and flax during their soda-anthraquinone (AQ) pulping and subsequent totally chlorine-free (TCF) and elementary chlorine-free (ECF) bleaching. For this purpose, residual lignins were isolated from pulps, analyzed by Py-GC/MS, 2D-NMR, and GPC, and their characteristics were compared to the “milled-wood” lignin of the raw materials. Soda-AQ pulping caused a preferential removal of S-lignin and cleavage of β–O–4′ linkages, but the structure of the residual lignin remained relatively similar to native lignin. TCF bleaching barely affected the lignin structure, and noticeable amounts of β–O–4′ linkages still occur in these pulps. In contrast, ECF bleaching caused strong modifications in the lignin structure with the complete removal of lignin markers in ECF-bleached sisal pulp. However, residual lignin was still present in ECF-bleached flax pulp, with a predominance of G- and H-lignin units and the presence of β–O–4′ linkages.