Abstract The critical demand for eco-friendly, renewable, and safe energy resources is an essential issue encountered in the contemporary world. The catalytic transesterification of plant oils into biodiesel was assessed as promising a technique for providing new forms of clean and safe fuel. Natural clinoptilolite was doped with Na+ ions by green chemical reactions between sodium nitrite and green tea extract, producing a novel modified structure (Na+/Clino). The Na+/Clino product had an enhanced total basicity (6.41 mmol OH/g), ion exchange capacity (387 meq/100 g), and surface area (312.7 m2 g−1), which qualified it to be used as a potential basic catalyst for the transesterification of palm oil. Transesterification tests were statistically assessed using a response surface methodology and a central composite design. Considering the effect of how the significant factors interact with each other, the synthetic Na+/Clino achieved a 96.4% experimental biodiesel yield after 70 min at 100 °C in the presence of 2.75 wt% catalyst loading and a 12.5:1 methanol-to-palm-oil ratio. Based on the optimization function of the statistical model, the performance of Na+/Clino can theoretically be enhanced to increase the yield to 98.2% by expanding the test time to 85 min and the loading value to 3 wt%. The product yielded by the Na+/ClinO process is of adequate technical properties, considering the international levels for standard biodiesel (EN 14214 and ASTM D-6751). Finally, the prepared green Na+ doped clinoptilolite had excellent recyclability as a heterogeneous basic catalyst and displayed higher efficiency than several species of previously studied heterogeneous and homogenous catalysts.