Nowadays, there is a growing consumer demand for non-dairy functional foods due to several health issues related to milk and dairy consumption and increasing vegetarianism. Following that trend, in the present study emmer-based beverages were developed after flour gelatinization, fortification with fruit juices (blueberry, aronia, and grape) and fermentation with the potential probiotic strain Lactiplantibacillus plantarum 2035. The produced beverages were subjected to a 4-week storage at 4 °C. The addition of juices significantly affected the physicochemical characteristics of the beverages, while resulting in increased red color. Total phenolic content (22.3–31.9 mg gallic acid equivalents 100 g−1) and antioxidant activity (94–136 μmol Trolox equivalents 100 g−1) were significantly higher in the case of aronia juice followed by blueberry and grape juice. All beverages showed high values of apparent viscosity and water-holding capacity. Lactiplantibacillus plantarum 2035 retained high viable counts during storage especially in beverages with fruit juices (>108 cells g−1 up to 21st day) revealing a positive effect of the juices. The obtained results show that emmer-based beverages fortified with fruit juices (aronia, blueberry, and grape) have a great potential as carriers of probiotics, prebiotics and other functional compounds and may be served as an ideal alternative to dairy products.