Abstract Structural modification of eucalypt pulp lignin was investigated in a totally chlorine-free (TCF) bleaching sequence including a laccase-mediator stage. This stage was applied after two oxygen delignification stages, and was followed by an alkaline peroxide stage. After two oxygen delignification stages, two more stages with a laccase mediator and alkaline peroxide were applied. The residual lignins were enzymatically isolated from the different pulps and analyzed by spectroscopic techniques and analytical pyrolysis. The latter revealed high amounts of syringyl units (>70%) in the lignins. 13C-1H heteronuclear single quantum correlation (HSQC) NMR indicated high amounts of β-O-4′ inter-unit linkages (>75% side-chains). Changes in lignin composition and inter-unit linkages were demonstrated in the course of the bleaching sequence. Moreover, oxidative modification of the major syringyl units was shown by C2,6-H2,6 HSQC correlations and by the presence of oxidized pyrolysis markers in pyrograms. The existence of both Cα keto and carboxyl groups in the residual lignin, together with normal (Cα-hydroxylated) units, was revealed by heteronuclear multiple bond correlation (HMBC) between aromatic H2,6 and side-chain carbons. These Cα-oxidized structures represent nearly 60% of total units in the lignin isolated from the enzymatically treated pulp. Analysis of residual lignin after the final peroxide stage compared with a simple alkaline treatment revealed that most of the oxidatively altered lignin was removed by the alkali used in the peroxide stage. Thus, the kappa number decreased and the final residual lignin was more structurally related to that found before the oxidative stages, although it contained less resinols and more carboxyl group-bearing units. However, the action of peroxide is necessary to attain the high brightness required (>90% ISO).