This study reports the development of a sustainable biocatalyst system for free fatty acid (FFA) production from cocoa bean shell (CBS) oil using Burkholderia cepacia lipase (BCL). CBS was explored as both a support material and a reaction substrate. Six immobilized systems were prepared using organic (CBS), inorganic (silica), and hybrid (CBS–silica) supports via physical adsorption or covalent binding. Among them, the covalently immobilized enzyme on CBS (ORG-CB) showed the most balanced performance, achieving a catalytic efficiency (Ke) of 0.063 mM⁻¹·min⁻¹ (18.6% of the free enzyme), broad pH–temperature tolerance, and over 50% activity retention after eight reuse cycles. Thermodynamic analysis confirmed enhanced thermal resistance for ORG-CB (Ed = 32.3 kJ mol⁻¹; ΔH‡ = 29.7 kJ mol⁻¹), while kinetic evaluation revealed that its thermal deactivation occurred faster than for the free enzyme under prolonged heating. In application trials, ORG-CB reached 60.1% FFA conversion from CBS oil, outperforming the free enzyme (49.9%). These findings validate CBS as a dual-function material for enzyme immobilization and valorization of agro-industrial waste. The results also reinforce the impact of immobilization chemistry and support composition on the operational and thermal performance of biocatalysts, contributing to the advancement of green chemistry strategies in enzyme-based processing.