This study investigated the potential application of an active biocatalyst from pawpaw (Carica papaya) trunk for the direct microwave irradiation‐aided transesterification of kariya (Hildegardia barteri) seed oil (KSO) with methanol to obtain biodiesel. The transesterification process involved was modeled, and the effects of the essential process input variables on the kariya seed oil methyl ester (KSOME) yield were examined, followed by the optimization of the input variables to maximize the KSOME yield, using the Taguchi orthogonal array design method. The biocatalyst was produced with a calcination process in a muffle furnace at 200–1000 °C, and each sample obtained was characterized by a scanning electron microscope equipped with energy‐dispersive X‐ray spectroscopy (SEM–EDX) to determine the best temperature. The calcined pawpaw trunk ash (CPTA) produced at the best temperature of 400 °C was further characterized using X‐ray diffraction (XRD), Fourier‐transform infrared (FTIR) spectroscopy, and physisorption analyses. The CPTA at 400 °C produced a strong catalytic activity due to its morphology, metallic composition (K (23.85%), and Ca (15.40%)), crystalline structure, the average pore size of 32.2 nm, and a surface area of 0.64 m2 g−1. The best operating conditions established for the transesterification process were a methanol / KSO molar ratio of 10.5:1, CPTA loading of 0.5 wt%, microwave heating power of 300 W, and reaction time of 2 min, with a maximum KSOME yield of 98.50 ± 0.60 wt%. The quality of the KSOME produced satisfied the American standard specifications for biodiesel. Both KSO and pawpaw trunk could serve as inexpensive feedstock for sustainable and renewable production of biodiesel. The intensification of the transesterification process using microwave irradiation drastically shortened the reaction time needed for maximum biodiesel yield. © 2021 Society of Chemical Industry and John Wiley & Sons, Ltd