In this study, we studied the conversion of Jatropha curcas oil to biodiesel by using three distinct reactor systems: microchannel, fixed bed, and microwave reactors. ZSM-5 was used as the catalyst for this conversion and was thoroughly characterized. X-ray diffraction was used to identify the crystalline structure, Brunauer–Emmett–Teller analysis to determine surface area, and temperature-programmed desorption to evaluate thermal stability and acidic properties. These characterizations provided crucial insights into the catalyst's structural integrity and performance under reaction conditions. The microchannel reactor exhibited superior biodiesel yield compared to the fixed bed and microwave reactors, and achieved peak efficiency at 60 °C, delivering high FAEE yield (99.7%) and conversion rates (99.92%). Ethanol catalyst volume at 1% was optimal, while varying flow rates exhibited trade-offs, emphasizing the need for nuanced control. Comparative studies against microwave and fixed-bed reactors consistently favored the microchannel reactor, emphasizing its remarkable FAME percentages, high conversion rates, and adaptability to diverse operating conditions. The zig-zag configuration enhances its efficiency, making it the optimal choice for biodiesel production and showcasing promising prospects for advancing sustainable biofuel synthesis technologies.