A continuously operating microwave heated milli reactor setup has been developed for performing reactions of highly microwave absorbing media in a controlled and energy efficient manner. The setup consists of a tubular reactor integrated with a heat exchanger. A microwave transparent liquid was used as coolant to extract the excess heat from the reaction mixture, thus controlling the temperature of the reaction mixture by avoiding overshoots and subsequent boiling. A reactor-heat exchanger shell and tube unit with a diameter of the inner tube of 3·10-3m and a shell of 7·10-3 m inner diameter has been manufactured in quartz. The unit size was defined based on simulation with a heat-transfer model for the microwave cavity part. Microwave heating was incorporated as a volumetric heating source term using the temperature-dependent dielectric properties of the liquid. Model predictions were validated with measurements for a range of 0.167·10-6 to 1.67·10-6 m3/s flow rates of coolant. The outlet temperature of both the reaction mixture and the coolant, were predicted accurately (tolerance of 3 K) and the process window was determined. The model for the reactor part provided the required length of the reactor for a solid (ion exchange) catalyzed esterification reaction. The predicted conversions, based on the obtained temperature profile in the reactor packed with the catalyst bed, known residence times and kinetics of the esterification reaction, were found to be in good agreement with the experimental results. Efficient utilization of microwave energy with heat recovery up to 20% of the total absorbed microwave power and heating efficiencies up to 96% were achieved. It has been demonstrated that the microwave heating combined with milli reactor flow processing provides controlled and energy efficient operation thus making it a viable option for a fine chemical production scale of 1 kg/day (24 hr period).