Fruit-based beverages have been considered excellent food vehicles for delivering prebiotics. However, the conventional thermal processes currently used to microbiologically and enzymatically stabilize these products may cause significant losses in their sensory, physicochemical, nutritional, and bioactive characteristics. Thus, in this study, we evaluate the effect of different levels of pressure (8, 15, and 21 MPa) and temperature (35 and 55 °C) on the characteristics of an inulin-enriched araticum beverage processed with non-thermal supercritical carbon dioxide (SC–CO2) technology. The temperature showed a significant effect on total soluble solids, pH, particle size distribution, and kinetic stability. In contrast, pressure affected only the particle size distribution. The interaction between pressure and temperature influenced the total soluble solids, pH, and particle size distribution. Color parameters, ζ-potential, and glucose and fructose contents were not modified after all SC–CO2treatments. Moreover, the SC–CO2treatments preserved the inulin molecular structure, thus maintaining its prebiotic functionality. Overall, the SC–CO2treatment did not alter the sensory, nutritional, and functional quality of the beverage, while improving its physical stability during storage. Therefore, non-thermal SC–CO2treatment can be an alternative to current conventional processes for stabilizing inulin-enriched fruit-based beverages.