Spray-drying technology plays an important role in developing matrices based on fruits to obtain beverages due to the low costs and high stability. Hence, two native fruits, calafate, well-known for the high anthocyanin content, and Chilean strawberry, with high ellagitannins content, were encapsulated separately and considered as ingredients to obtain beverages. In this work, the purpose was to predict the adequate conditions to achieve the stabilization of the bioactive compounds and antioxidant capacity in ingredients after different treatments of temperature (90 and 120°C) or wall material content (10 and 30% maltodextrin) in native Chilean berries. By using a predictive model, we sought insights into the loss of bioactive compounds in calafate and Chilean strawberry, and slight differences between the two working temperatures in relation to the loss of bioactive compounds were observed. In contrast, the use of different maltodextrin contents presented more significant results, since by increasing the proportion of wall material, the bioactive compounds were more adequately protected. These data demonstrate that models to predict the right conditions, of temperature or wall material, to formulate matrices that serve as a basis for the development of beverages can be a useful tool.