The Fourth Industrial Revolution (4IR) drive is accompanied by substantial advancements in the use of technological materials, resulting in massive increases in the quest for a waste-free environment. Watermelon seeds, often discarded as agricultural waste, are a readily available byproduct that can be valorized through biodiesel production, reducing waste while contributing to renewable energy goals and circularity principles. Modification of catalysts for improved biodiesel yield and quality has also been attempted through scientific experimentation. In converting watermelon seed oil to biodiesel, zeolites enhance the transesterification process by improving reactant diffusion, increasing conversion efficiency, and producing higher-purity fuel. This work aims to produce biodiesel from watermelon seed oil using a kaolin-based zeolite as a heterogeneous catalyst. This catalyst is promising for the transesterification reactions of oils due to its economic benefits. Moreso, it is environmentally benign and can be unlike homogeneous catalysts. The transesterification was optimized by varying the reaction time (45 to 105 min), methanol-to-fatty acid molar ratio (1.5:1 to 7.5:1), reaction temperature (55 to 75 °C), and catalyst concentration (0.25 to 1.25 wt%) using the Response Surface Methodology (RSM). It was found that the highest yields (92% and 90%) were achieved for both predicted and actual values, with R² values of 0.9510, respectively. Comparison of the obtained biodiesel quality with relevant ASTM standards yielded positive results, with kinematic viscosity, cetane number, flash point, and free fatty acid of 4.4 mm²/s, 62.4, 156 °C, and 0.37, respectively.