The production of biodiesel has increased globally during the last decade to overcome the problems of increasing prices of petro-diesel and the depletion of fossil fuels. The present study aimed to utilize agro-waste sugarcane bagasse (SCB) to synthesize a heterogeneous acid catalyst for biodiesel production using waste cooking oil. Waste sugarcane bagasse was converted into biochar through partial carbonization and activated via sulfonation by using acid solutions of different concentration i.e., 1M, 3M, 5M and concentrated sulfuric acid at a sulfonation temperature of 180 °C for 5 h. The prepared catalysts were characterized by using Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), scanning electron microscopy (SEM), the Brunauer�Emmett�Teller (BET) technique, X-ray diffraction (XRD), and the Carbon, Hydrogen, Nitrogen and Sulfur (CHNS) analyzer. The prepared catalyst exhibited an excellent surface area of 20.78 m2 g�1 and a total acid density of 3.94 mmol g�1. The biodiesel production process was optimized by varying reaction temperature from (40�70 °C), methanol to oil molar ratio (5:1�20:1), catalyst loading (1�7 wt.) and reaction time (5�25 min) by using a microwave reactor. The maximum conversion of 95.45 and yield of 92.12 was obtained under optimum conditions: catalyst loading 5 wt, methanol-to-oil molar ratio (15:1), temperature (60 °C) after 15 min. The results of the experiments were validated by using response surface methodology, which validated the predicted model. The kinetic study of experiments showed that the use of sulfonated catalysts lowered the activation energy (10.5 kJ mol�1) and reactants attained an equilibrium point after a short interval under microwave heating. Reusability of catalyst up to seven cycles with 77.34 yield of biodiesel using low-grade feedstock showed that the catalyst is stable and can be used for sustainable biodiesel production. The utilization of wastes for catalyst synthesis and for biodiesel production can help to minimize the overall production cost of biodiesel. © 2021 Society of Chemical Industry and John Wiley & Sons, Ltd. © 2021 Society of Chemical Industry and John Wiley & Sons, Ltd