Lignin is a highly abundant, renewable biopolymer with the potential to replace fossil-based aromatic building blocks in polymeric materials. However, the structural complexity of lignin, arising from its heterogeneous interunit linkages and irregular architecture, complicates the assessment of structure–property relationships. In this work, a lignin with a high content of the β-O-4′ interunit linkage, prevalent in native lignin, is utilized to reveal how the molecular structure governs the mechanical performance of lignin-based thermosets. The lignin was modified with allyl functionalities and thermally cross-linked using thiol–ene chemistry. A comprehensive structural analysis and characterization show that maintaining a high β-O-4′ content results in networks that exhibit both high modulus and ductile behavior (E: 1–3 GPa, and ε_b > 10%). This effectively addresses the trade-off between stiffness and ductility often encountered in technical lignin-based materials, having strain-at-break values below 4%. These findings highlight molecular structure as a crucial parameter for optimizing mechanical performance and tailoring lignin-based materials for high-performance applications, such as organic coatings or adhesives.