Nowadays, there is growing interest for the development of enriched dairy products with phenolic compounds derived from edible sources, mainly due to their safety and potential health benefits. Following that trend, in the present study, fruit juices (blueberry, aronia, and grape) were supplemented into yogurt as functional ingredients. The main physicochemical characteristics (pH, reducing sugars, acidity, color, and syneresis), total phenolic content, antioxidant activity, and viability of yogurt starters were monitored during production and storage. The use of juices had no significant effect on milk acidification rate and on the main physicochemical characteristics of yogurts, while resulted in increased red color. Total phenolic content increased from 30 to 33% (grape and aronia) and up to 49% (blueberry), while similar results were observed in antioxidant activity. Similar values of syneresis were presented in all yogurts, probably due to exopolysaccharide producing starter culture. Streptococcus thermophilus retained high viable counts during storage especially in yogurts with fruit juices (>108 cells g−1) revealing a possible prebiotic effect of juices. The results obtained from this study show that fruit juices (aronia, blueberry, and grape) have potential to be used in yogurt production in order to optimize the benefits of probiotic products with high phenolic compound intake.