Due to recent interest in the potential of probiotics as health promoters and the impact of health and environmental concerns on eating habits, non-dairy probiotic food products are required. This study aimed to evaluate the viability of different probiotic microorganisms in peach and grape juice (PGJ) with or without the prebiotic inulin and their antimicrobial activity against the foodborne pathogen Listeria monocytogenes and the juice spoilage microorganism Saccharomyces cerevisiae. Firstly, the viability of seven probiotic strains was studied in PGJ with an initial concentration of 107 CFU/mL for 21 days at 4 °C and for 3 days at 37 °C. In parallel, the physicochemical effect, the antimicrobial effect and the lactic acid production in PGJ were evaluated. Secondly, the probiotic with the best viability results was selected to study its antimicrobial effect against L. monocytogenes and S. cerevisiae, as well as ethanol and acetaldehyde production by the latter. L. casei showed the highest viability and grew in both refrigerated and fermentation conditions (1 log), produced the greatest lactic acid (5.12 g/L) and demonstrated in vitro anti-Listeria activity. Although the addition of the prebiotic did not improve the viability, lactic acid production or anti-Listeria activity of the probiotics, under the conditions studied, the prebiotic potential of inulin, support the design of a synbiotic juice. Finally, although none of the probiotic, fermentation products, or postbiotics showed any antimicrobial activity against L. monocytogenes or S. cerevisiae, the addition of L. casei to the PGJ significantly reduced the production of S. cerevisiae metabolite ethanol (29%) and acetaldehyde (50%). L. casei might be a suitable probiotic to deliver a safe and functional PGJ, although further research should be carried out to determine the effect of the probiotic and fermentation on the nutritional profile of PGJ.