Great advances have been recently made in the area of miniaturization of systems. One of the most important aspects of these microdevices is the mixing of the reacting species, which will determine its conversion to the desired product. These microdevices have been successfully applied in the synthesis of biodiesel, mainly due to increased conversion of reactants in a short residence time. Oils derived from non-edible oil seeds are promising feedstock sources for biodiesel, especially Jatropha species. As a result, this paper numerically studied the mixing and reaction of Jatropha curcas oil and ethanol in micromixers for the production of biodiesel. Three types of micromixers were studied: T-micromixer, Cross-micromixer and Double-T-micromixer. The efficiency of each type was analyzed using a mixing index, which is calculated using the variation of mass fraction, and the conversion of oil. The mixing of the fluid was analyzed with different Reynolds numbers and the conversion of oil was analyzed for different Reynolds numbers and residence times. All showed excellent degree of mixture for low Reynolds numbers, with the Cross-micromixer showing the highest degree of mixing. By increasing the Reynolds number the mixing in the T-micromixer was increased, reduced in the Double-T-micromixer and did not affect the mixture in the Cross-micromixer. It was observed that the conversion obtained in all micromixers is practically constant and is not affected by the variation of Reynolds number studied (10–100). The Cross-micromixer presented the best reaction yield. An increment in residence time increased the conversion of oil. This work numerically demonstrated the possibility of using J. curcas as a feedstock for synthesis of biodiesel in microchannels. Display omitted •The J. curcas-ethanol mixing and reaction in micromixer are simulated.•Three types of micromixers were studied: T-, Cross- and Double-T-micromixer.•The Cross-micromixer showed the highest mixing index, with average values of 0.99.•The reaction are controlled by mixing and reaction kinetics processes.•The residence time played an important role in the conversion of the oil.