This study explores the sustainable production of biodiesel from nonedible Phyllanthus maderaspatensis seed oil (highest oil content of 35%, FFA 0.87 mg/KOH), utilizing an innovative green synthesis approach for chromium oxide nanoparticles derived from the waste fruit parts of Aubergine for the very first time in the current work. In pursuit of alternatives to fossil fuels, our research underscores the environmental and socio‐economic benefits of biofuels, particularly in reducing greenhouse gas emissions. The optimized process yielded a 92% biodiesel conversion under conditions of a 9:1 methanol‐to‐oil ratio, 0.135 wt.% catalyst concentration, and a reaction duration of 150 min at 80°C. Comprehensive analysis techniques, including XRD, FTIR, SEM, EDX, Zeta analysis, differential reflectance spectroscopy (DRS), GC–MS, and NMR (1H, 13C), were employed to characterize the synthesized nanocatalyst and biodiesel product. The biodiesel's fuel properties, such as acid value, fire point, pour point, viscosity, kinematic density, sulfur content, and cloud point, were rigorously tested, demonstrating compliance with international standards (ASTM D‐6571, EN 14214, and GB/T 20828‐2007). The use of P. maderaspatensis seed oil, an economical and environmentally friendly feedstock, in conjunction with a cost‐effective nanocatalyst, presents a viable pathway for the sustainable and scalable production of biodiesel. This study contributes to the advancement of bioproducts for a sustainable bioeconomy by demonstrating an integrated approach to bioenergy production that leverages biotechnological innovations and addresses both environmental and socio‐economic dimensions.