Consumer interest toward natural ingredients is creating a growing trend in the food industry and research for the development of natural products such as colorants, antimicrobials and antioxidants. Semi-processed frozen prickly pear (Opuntia ficus-indica (L.) Mill.) juices (PPJs), obtained from three cultivars with white, red and yellow pulp, with different harvest times (“Agostani” and “Bastardoni”), were characterized for betalains, total phenolics, flavonoids, carotenoids, antioxidant capacity (by 2,2-diphenyl-1-picryl-hydrazyl-hydrate (DPPH)) and antimicrobial potential against foodborne pathogenic bacteria. Through chemical assays, PPJs showed high contents of total polyphenols, flavonoids and betalains and marked antioxidant capacity. PPJs from the first harvest (“Agostani”) revealed the significantly highest amount of polyphenols in white cultivar and of betacyanin and betaxanthin in yellow and red cultivars; antioxidant capacity was significantly higher in “Agostani” PPJs than in “Bastardoni” ones. Regarding antimicrobial potential, all PPJs revealed good antibacterial activity, particularly against Salmonella enterica as evidenced by the widest inhibition haloes. These results encourage the suitability of the first flowering prickly pear fruits, with low market value as fresh fruit but with high nutritional features, to be processed as semi-finished product. In particular, its use as ingredient in foods with high risk of Salmonella contamination may act as a natural preservative.