The valorization of underutilized organic waste into high-value polymeric materials is a growing topic in Thailand's industrial polymer production sector, addressing critical ecological challenges. Lignin, an abundant aromatic biopolymer found in agricultural wastes like coconut shells, has significant potential for producing high-value chemicals and contributing to a circular economy. However, its complex structure, characterized by sensitive C-O bonds, necessitates selective extraction to develop useful aromatic molecules for biotechnological applications. This study investigated the catalytic performance of hydrochloric acid in the organosolv treatment of coconut shells. Lignin was hydrolyzed in a 70% ethanol solution with 2.2% (w/v HCl) at 190 °C for 90 min, yielding up to 96% lignin. The chemical structure of lignin was characterized and discussed. Fourier-transform infrared (FT-IR) spectroscopy revealed a high intensity of hydroxyl groups, indicating the breakdown of lignin–carbohydrate linkages and interlinkages. The lignin consists of syringyl (S), guaiacyl (G), and p-hydroxyphenyl (H) units, classifying it as a grass-type (HGS). Methoxyl groups were also identified in the coconut shell monomeric units, suggesting minimal modification of the native lignin structure. Additionally, the resulting β–O–4 linkage-rich lignin fractions exhibited enhanced biological reactivity compared to commercially available lignin, demonstrating UV absorption capacity and antibacterial properties. This work proposes a sustainable biorefinery approach to transform agro-wastes into valuable resources through lignin extraction, facilitating the creation of bioactive compounds for innovative applications in cosmetics and health products.