The microwave irradiation and the droplet-based millifluidic process are coupled to explore the microwave heating of individual droplets in polymer chemistry. The continuous phase is a microwave-inert oil while the reactive droplets contain hydrosoluble monomer and initiator in an aqueous medium. Microwaves affect directly and preferentially the molecules within the reactive droplets. Addressing the challenge of a suitable millifluidic system coupled to microwave irradiation, the device has been design to answer geometrical and chemical specifications. To get around the issue of the measurement and the control of the droplet temperature while flowing inside the microwave cavity, the use of a chemical probe has been developed (azoic compound) with an assessment in the range 50–90 °C. The polymerization in the droplet-based millifluidic device and microwave irradiation has been successfully performed on acrylic acid under 90 W at a temperature within the range 60–70 °C.