This study aimed to develop a functional powder using whey and milk matrices, leveraging the protective capacity of chia-alginate hydrogels and the advantages of electrohydrodynamic spraying (EHDA), a non-thermal technique suitable for encapsulating probiotic cells under stress conditions commonly encountered in food processing. A hydrogel matrix composed of chia seed mucilage and sodium alginate was used to form a biopolymeric network that protected probiotic cells during processing. The encapsulation efficiency reached 99.0 ± 0.01%, and bacterial viability remained above 9.9 log CFU/mL after lyophilization, demonstrating the excellent protective capacity of the hydrogel matrix. Microstructural analysis using confocal laser scanning microscopy (CLSM) revealed well-retained cell morphology and homogeneous distribution within the hydrogel matrix while, in contrast, scanning electron microscopy (SEM) showed spherical, porous microcapsules with distinct surface characteristics influenced by the encapsulation method. Encapsulates were incorporated into beverages flavored with red fruits and pear and subsequently freeze-dried. The resulting powders were analyzed for moisture, protein, lipids, carbohydrates, fiber, and color determinations. The results were statistically analyzed using ANOVA and response surface methodology, highlighting the impact of ingredient ratios on nutritional composition. Raman spectroscopy identified molecular features associated with casein, lactose, pectins, anthocyanins, and other functional compounds, confirming the contribution of both matrix and encapsulants maintaining the structural characteristics of the product. The presence of antioxidant bands supported the functional potential of the powder formulations. Chia-alginate hydrogels effectively encapsulated , maintaining cell viability and enabling their incorporation into freeze-dried beverage powders. This approach offers a promising strategy for the development of next-generation functional food gels with enhanced probiotic stability, nutritional properties, and potential application in health-promoting dairy systems.