In this study, the combination of sequential solvent fractionation of technical Kraft lignin was followed by allylation of most OH functionalities to give highly functional thermoset resins. All lignin fractions were highly functionalized on the phenolic (≥95%) and carboxylic acid OH (≥85%) and to a significant extent on the aliphatic OH moieties (between 43 and 75%). The resins were subsequently cross-linked using thiol-ene chemistry. The high amount of allyl functionalities resulted in a high cross-link density. Dynamic mechanical analysis measurements showed that the thioether content, directly related to the allyl content, strongly affects the performance of these thermosets with a glass transition temperature (Tg) between 81 and 95 °C and with a storage modulus between 1.9 and 3.8 GPa for all thermosets. The lignin fractions and lignin-based thermosets’ morphology, at the nanoscale, was studied by wide-angle X-ray scattering measurements. Two π-π stacking interactions were observed: sandwich (≈4.1-4.7 Å) and T-shaped (≈5.5-7.2 Å). The introduction of allyl functionalities weakens the T-shaped π-π stacking interactions. A new signal corresponding to a distance of ≈3.5 Å was observed in lignin-based thermosets, which was attributed to a thioether organized structure. At the same time, a lignin superstructure was observed with a distance/size corresponding to 7.9-17.5 Å in all samples.