The search for environmentally friendly alternatives to conventional fossil fuels has been intensified by the global shift toward sustainable energy sources. With over 95% of the fuel market dominated by petroleum-based products, concerns regarding their limited biodegradability and high eco-toxicity have been escalated. In response, there is a growing demand for biobased solutions that can mitigate pollution and reduce greenhouse gas emissions. In this study, the synthesis of biodiesel from waste almond seed oil (WCO) was focused on, utilizing an innovative bifunctional catalyst derived from waste animal bones and almond shells. The efficacy of the catalyst synthesized from these unconventional materials was confirmed through rigorous characterization techniques, including scanning electron microscopy (SEM), X-ray diffraction (XRD), X-ray fluorescence (XRF), Fourier transform infrared (FTIR) spectroscopy, and Brunauer, Emmett, and Teller (BET) analysis. The physicochemical properties of WCO and the resulting biodiesel were evaluated according to ASTM D6751 and EN 14214 standards. To optimize the catalytic process, Box Behnken Design (BBD) was employed to explore the effects of key parameters: reaction temperature (40-60°C), reaction time (60-90 minutes), catalyst loading (0.5-1.5 wt%), and methanol-to-oil ratio (6:1-18:1). Remarkably, under optimal conditions, an impressive biodiesel yield of 86.2% was achieved. Specifically, the optimal parameters were a Methanol:Oil Ratio of 6.026, Catalyst Loading of 1.49917 wt%, Reaction Time of 66.8179 minutes, and Temperature of 59.9806°C. The potential of utilizing waste materials for sustainable biodiesel production is underscored by our findings. The bifunctional catalyst developed in this study represents a cost-effective and environmentally friendly alternative to conventional catalysts, contributing to cleaner fuel production methods.