<p>Efficient lignin valorization into high-performance materials is hindered by cleavage of β–O–4 linkages and condensation during acidic fractionation. Here, an amino acid–assisted molecular design using histidine and aspartic acid stabilizes and functionalizes dilute-acid sugarcane bagasse lignin, enabling integrated conversion into functional carbon materials and reinforced three-dimensional (3D)-printed poly(lactic acid) (PLA) composites. Structural and interfacial analyses showed that histidine produced a less-condensed, β–O–4-rich lignin structure, with the β–O–4 content increasing from 35.8/100 Ar in unmodified dilute-acid lignin to 49.3/100 Ar in histidine-lignin and 43.6/100 Ar in aspartic acid-lignin, while condensed S-unit content decreased from 6.3% to 1.9% and 2.4%, respectively. As for thermochemical behavior, the histidine and aspartic acid-modified lignin yielded 33.1% and 31.0% of phenolic-rich oil, respectively, with both hierarchically porous nitrogen-doped biochars. The histidine-derived biochar achieved a Brunauer–Emmett–Teller surface area of 364.8 m² g^-1 (versus 61.4 m² g^-1 for the unmodified lignin-derived char) with pyridinic, pyrrolic, and graphitic nitrogen species. When blended with PLA and processed into filaments for fused deposition modeling, histidine-functionalized lignin acts as an active compatibilizer, improving dispersion and polymer–filler interfacial cohesion; at an optimal loading of 0.2 wt%, the tensile strength, elongation at break, and toughness of 3D-printed parts increase by 40%, 89%, and 217.8%, respectively, compared with PLA composites containing unmodified lignin. This work links fractionation-stage molecular stabilization to structure–property design in polymer composites and lignin-derived hybrid carbon materials, offering a scalable route to value-added, bio-based hybrid materials.</p> Graphical abstract <p></p>