Optimization of biodiesel production requires fundamentals-based kinetic and reactor models. A liquid–liquid reactor requires reaction rate model including mass-transfer effects. Earlier studies have not analyzed such an effect in detail and thus cannot be used for scale-up and design. This work develops a two-scale model for design and scale-up. The intrinsic rate constant, fit from experimental data, is approximately 300 times larger than the apparent one. The model results for microchannel and stirred-batch reactors agree well with the experimental data and indicate that the former requires approximately 720 times shorter residence time than the latter. Scaling-up of an agitated-batch reactor to industrial scale by keeping tip speed constant provides lower performance due to inadequate power. In contrast, scaling-up with constant power/volume provides higher performance due to oversupply power. The two-scale model is used to adjust agitation speed for achieving performance similarity during scale-up. The corresponding power lies in between the two above-mentioned values.