Herein, we report successful non-thermal pasteurization of fruit juices (watermelon and red grape juices) in a flow-through pulsed light (PL) reactor. Impact of PL reactor configuration (annular/coiled tube), product flow rates (14–75 L/h) and pulse frequency (1–5 Hz) on the inactivation of Escherichia coli ATCC 29055, Listeria innocua ATCC 33090, and Clostridium sporogenes ATCC 7955 in red grape (pH = 3.37) and watermelon juice (pH = 5.02), and changes in quality and nutritional parameters, was explored. >5 and > 7 log10 microbial reductions were achieved in annular and coiled reactor respectively, demonstrating PL's potential in juice pasteurization. Watermelon juice exhibited higher microbial inactivation, while E. coli was found to be most susceptible. The inactivation kinetics using three different models were compared wherein ‘log-linear plus tail model’ showed the best fit. During PL processing, there were minor changes in pH and colour of both juices, whereas nutritional parameters (total anthocyanins, total phenolics, antioxidant capacity, vitamin C, trans-resveratrol, and lycopene content) decreased significantly (p < 0.05) by up to 39.1%, 62.2%, 53.8%, ∼70%, 82%, and 46.8%, respectively, yet at levels lower than conventional thermal pasteurization. These results shall inspire commercialization of PL based fruit beverage pasteurization systems.