Novel technologies that involve non-thermal processes have been investigated in the last two decades as full or partial alternatives to conventional heat treatment. The main objective of this study was to evaluate the survival of single or strain cocktail of Escherichia coli, Saccharomyces cerevisiae, and a yeast cocktail in orange (pH 3.5; 9°Brix) and/or apple (pH 3.1; 12°Brix) juices and in 0.1% w/w peptone water processed by two non-thermal techniques: high-intensity ultrasound (USc) and/or short-wave ultraviolet radiation (UV-C). USc treatments (20 kHz, 95 µm-wave amplitude) were performed using a stainless steel continuous flow cell with a 13-mm probe (0.2 L/min; 40°C). The UV-C device consisted of a 90-cm long UV-C-lamp (100 W) placed inside a glass tube leaving an annular flow space (0.2 L/min; 40°C). Inoculated systems were recirculated through simultaneous or consecutive USc and UV-C devices and samples were taken at preset time intervals. Microbial populations were monitored by plate count technique. In peptone water and apple juice, UV-C radiation provoked higher E. coli ATCC 35218 inactivation than USc treatment. E. coli ATCC 35218 and its cocktail were more sensitive than S. cerevisiae KE162 and the cocktail of yeasts. UV-C efficiency was highly dependent on media nature. The poor single effect of UV-C light in orange juice was enhanced by the combination with USc. Combined treatment was more effective in simultaneous rather than in a series of USc−UV-C arrangement.