Continuous flow microwave heating is a promising alternative to conventional heating for aseptic processing of low-acid vegetable purees. However, non-uniform temperature distribution and control of processing parameters are the major hurdles in the implementation of continuous flow microwave heating. This study was undertaken to overcome issues associated with the scale-up of a continuous flow microwave system from pilot plant scale to industrial scale and to conduct extended run times of 8 h based on the procedure developed. Dielectric properties and cross-sectional temperature profiles were measured during processing of green pea puree and carrot puree from 20 to 130 °C in a 5-kW continuous flow microwave system. During processing of green peas, cross-sectional temperature differences of 8.6 and 5 °C were observed at the outlet for center temperatures of 50 and 130 °C respectively. These temperature differences were 32.9 and 3.6 °C for carrot puree. For process scale-up, green pea puree and carrot puree were processed in a 60-kW microwave system with the objective of successful operation for at least 8 h. Static mixers, installed at the exit of each of the microwave applicators, improved temperature uniformity for both purees. Successful completion of processing the purees for 8 h in the 60-kW microwave system showed the potential for the scale-up of a continuous flow microwave system from pilot plant scale to industrial scale.