The rapid depletion of fossil fuel resources and climatic changes has triggered the researchers' attention to find an alternative and renewable energy source. Thus, biodiesel has been recognized as a potential alternative to petrodiesel for its biodegradability, non-toxicity, and environment-friendly attributes. In this study, an efficient and recyclable Cu–Ni doped ZrO2 catalyst was synthesized and used to produce biodiesel from a novel non-edible caper (Capparis spinosa L.) seed oil. The synthesized catalyst was characterized by x-ray diffraction, fourier-transform infrared spectroscopy, scanning electron microscopy, and energy dispersive x-ray analysis. The catalyst was reused in four consecutive transesterification reactions without losing any significant catalytic efficiency. Transesterification reaction conditions were optimized via response surface methodology based on Box-Behnken design for predicting optimum biodiesel yields by drawing 3D surface plots. Maximum biodiesel yield of 90.2% was obtained under optimal operating conditions of 1:6 M ratio of oil to methanol, reaction temperature of 70 °C, reaction time of 1.5 h, and 2.5% catalyst loading. Fourier-transform infrared spectroscopy, gas chromatography–mass spectrometry, and nuclear magnetic resonance (1H and 13C) analysis confirmed the high quality of biodiesel produced from non-edible caper (Capparis spinosa L.) seed oil. The fuel properties of the produced biodiesel were also found, such as kinematic viscosity (4.17 cS T), density (0.8312 kg/L), flash point (72 °C), acid no (0.21 mgKOH/g) and sulphur content (0.00042 wt%). These properties were matched and are in close agreement with the International Biodiesel Standards of European Union (EU-14214), China GB/T 20,828 (2007), and American (ASTM6751). Thus, non-edible Capparis spinosa L. seed oil and Cu–Ni doped ZrO2 catalyst appeared to be highly active, stable, and cheap candidates to boost the future biodiesel industry.