Transesterification is the most common method for biodiesel production, typically occurring with excess alcohol to shift the reaction balance towards the products. After the reaction, this alcohol can be removed and recovered. On both macro and micro scale, such process occurs in evaporators or even in distillation columns. In view of the above, this article intends to apply a microchannel heat exchanger based on a Peltier module on the separation of excess alcohol from the biodiesel in microscale. Three variables were assessed in the process: temperature, fluid flow rate in the micro-exchanger and alcohol/biodiesel molar ratio. The results revealed that temperature has a positive effect on the evaporation efficiency, whereas the variables of flow rate and molar ratio showed a negative effect on the process. Accordingly, we have thus shown the possibility of using heat micro-exchangers on the separation of excess alcohol from biodiesel. (C) 2017 Institution of Chemical Engineers. Published by Elsevier B.V. All rights reserved.