Abstract The depletion of fossil fuel and the distressing environmental condition originated from the massive consumption of nonrenewable energy has urge towards the seeking for a cleaner and renewable energy source. Numerous forms of renewable energy have been developed over the past few decades and biodiesel emerged as one of the prospective candidate. The demand for global biodiesel production has been steadily growing. In line with that, researches around the world are racing towards making biodiesel technology more sustainable and economically viable process. In this investigation, the development of biodiesel from palm fatty acid distillate via the esterification process using sulfonated chicken bone and cow bone catalyst assisted by microwave irradiation was conducted (replacing the conventional oven heating). Subsequently the bones were calcined at 900 °C and then sulfonated. The synthesized catalysts were characterized using X-Ray diffraction, Fourier transform infrared spectroscopy, field emission scanning electron microscope, Brunauer–Emmett–Teller and temperature-programmed desorption. The reaction was prepared with a catalyst loading of 1 % to 6 % and a molar ratio of 2:1 to 25:1 for methanol:PFAD, while the reaction time was conducted for 30–240 mins and the reaction temperature was kept at 70 °C for each experiment set. In addition, a catalyst loading of 5 wt% and molar ratio of 20:1 for methanol:PFAD with the reaction time of 180 mins and reaction temperature of 70 °C were used as optimal condition parameters. For the sulfonated chicken bone catalyst, the percentage yield and conversion of biodiesel were 80.8% and 98.2%, respectively. In contrast, the percentage yield and conversion rate reached to 81.5% and 97.7%, respectively, for the the sulfonated cow bone catalyst. The biodiesel properties obtained were in accordance with ASTM standards. The percentage of FAME content was determined utilizing gas chromatography. The bones have been shown to be appropriate sustainable precursors for the synthesis of a novel, highly effective heterogeneous acid catalyst for biodiesel development.