During the past decade, the application of new technologies such as high pressure, ultrasound, pulsed electric fields, shortwave ultraviolet C (UVC) light, and microwave (MW) has been thoroughly investigated for food processing. Combinations of UVC light with different technologies have been previously investigated, with promising results when combined with mild thermal treatments. The objective of this work was to study the inactivation of Saccharomyces cerevisiae and Escherichia coli inoculated in pomegranate juice within a unit of UVC-coiled (254 nm) equipment and the continuous-flow MW (876 W energy output). Individual and combined treatments were evaluated at two flow rates through the tested systems. The combined technologies notably improved the inactivation of the target microorganisms. Our findings indicated a synergistic effect between the systems, respectively yielding 6.1 and 5.5 log-cycle reductions in the yeast and bacteria for the UVC-MW treatment with a flow rate of 400 ml/min. When increasing the flow rate, different results were observed, depending on the temperature pattern. A dynamic model was obtained for MW temperature profiles and residence time distributions for the studied systems to better explain the obtained results. Practical applications Nowadays, alternative food-processing technologies are under research to obtain safe, fresh-tasting, and nutritive foods using mild temperatures or no heat. This work aimed to evaluate a configuration wherein a unit of UVC-coiled equipment was coupled with a continuous-flow MW system. Processing times for treating juices can be significantly reduced by combining a UVC coiled equipment with a continuous flow microwave system, because of the enhanced effect of UVC at mild temperatures and the faster heating due to the MW. Its potential implementation will allow the food industry to offer minimally processed products with clean labels and at an affordable cost. 1 | INTRODUCTION Conventional heat treatments for the pasteurization of juices have many advantages. For instance, they guarantee food safety by increasing the product shelf life through the inactivation of enzymes and microorganisms. However, thermal processing has some disadvantages, since it can induce flavor losses and deterioration in the natural quality of fresh juices (Rabie, Soliman, Diaconeasa, &