Mixing is an essential operation in many microfluidic devices. Droplet-based micromixers utilize droplets for mixing enhancement. In the present study, a novel three-dimensional simulation is conducted which has the ability to capture not only the mixing process, but also the chemical reactions inside liquid droplets. This two-phase model is used for simulating the reacting flow inside a serpentine microchannel and explores the effects of droplet size and reaction rate on the production and consumption of species in droplets. It is observed that the chemical reaction in each droplet, begins from its front area. Furthermore, it is shown that the production of species does not depend on water fraction (ratio of water flow rate to total flow rate) and for all droplet sizes, only depends on the reaction rate. Moreover, different transient generated vortices and secondary flows are studied in the presence and absence of droplets and explained in details based on the position of droplets. It is found that during the passage of droplets through a microchannel bend, the number of cross-sectional vortices changes and the velocity magnitude in these secondary flows increases dramatically. (C) 2017 Elsevier Ltd. All rights reserved.