The escalating demand for renewable energy necessitates the exploration of novel, non-edible feedstocks for biodiesel production that do not compete with food security. This study investigates the potential of Pinus eldarica Medw., a Near Threatened endemic conifer of the Caucasus Biodiversity Hotspot, as a sustainable feedstock for fatty acid methyl ester (FAME) production. Seeds collected from naturally occurring populations on the Eilyar-Oyugu range in Azerbaijan were processed by Soxhlet extraction to recover the seed oil, the yield of which compares favourably with that of several conventional non-edible feedstocks such as Acacia senegal, Jatropha curcas, and Calophyllum inophyllum (the last of which, however, carries a high free fatty acid content). A green magnesium oxide (MgO) nanocatalyst was biosynthesized from P. eldarica bark extract via an environmentally benign route, eliminating the need for hazardous reducing agents. Transesterification of the seed oil using the green MgO nanocatalyst achieved up to 96% FAME conversion efficiency. The physicochemical properties of P. eldarica biodiesel were evaluated against the ASTM D6751 and EN 14214 international standards. Furthermore, life cycle assessment perspectives and blending strategies (e.g., B20) were discussed as pathways to improve economic viability and engine compatibility. This research contributes a dual-purpose framework that simultaneously advances biofuel science through green catalysis innovation and supports the conservation of a critically important endemic species within a recognized global biodiversity hotspot.