The present study focused on the development of gel-based capsules from sodium alginate and the fresh juice from different berries: chokeberry, sea buckthorn, and blueberry. Obtained through the extrusion method, the macrocapsules were added into yogurt, a well-known and consumed dairy product. In order to establish the changes that can occur for the food product, the samples were tested over 7 and 15 days of storage in refrigeration conditions. According to the results, the antioxidant activity increased during storage and gels can represent a good option for bioactive substances’ encapsulation. Sensorial analysis performed indicated that consumers are open to consuming yogurt berry capsules and, according to the results observed in the scientific literature, they no longer rejected the product due to the bitterness and sourness of sea buckthorn or aronia. Sea buckthorn capsules were brighter (L*) than chokeberry and blueberry capsules due to carotene content and dark colors. Minimal diameter variations and small standard deviations (SD = 0.25/0.33) suggest that extrusion methods and the Caviar box are good for gel capsule development. Yogurt luminosity varied with capsules; control had the highest, followed by sea buckthorn yogurt. Samples with chokeberry and blueberry (dark) capsules had lower luminosity. Over 8 and 15 days, luminosity slightly decreased, while a* and b* (hue and saturation) increased. Post-storage, the sample with chokeberry capsules showed a light purple color, indicating color transfer from capsules, with increased antioxidant activity. Differences between the samples and control were less pronounced in the sample with sea buckthorn capsules. Values for color differences between yogurt samples during the storage period revealed the most significant difference during the first storage period (day 1–8), with blueberries showing the lowest difference, indicating the stability of the blueberry capsules’ wall during storage.