The study investigated the suitability of a novel strain Lactiplantibacillus plantarum EK11 for obtaining fermented tomato and beetroot juices with improved functional potential. EK11 had the capability of dynamic acidification of pasteurized vegetable beverages. The lowest values of pH were noted in juices after 48 h of fermentation with the probiotic L. plantarum 299v (pH=3.72±0.01 in beet juice and pH=3.43±.0.01 in tomato juice). The fermentation increased the lycopene content in tomato juices from 27.90±0.31µg mL−1 (after 24-h fermentation by strain EK11) to 116.86 ±0.19 µg mL−1 (final products obtained using strain 299v after 7-day cold storage). The process contributed to changes in the betanin and vulgaxanthin-I concentration in beetroot beverages. All fermented products exhibited antioxidative activity, i.e. 50% inhibition of 1,1-diphenyl-2-picrylhydrazyl free radicals. Moreover, three genes involved in the biosynthesis of bacteriocins were detected in the novel strain EK11, which exhibits functional and technological potential for the production of fermented foods.