This study evaluated the effect of ultrasound (US) as soft thermal processing or thermosonication technology to improve the properties of a functional beverage made from noni (Morinda citrifolia) and carambola (Averrhoa carambola). A 3² factorial design was applied with ultrasound temperatures (50–60°C) and times (25–35 min). Physicochemical, bioactive, and colorimetric parameters were analyzed, modeling their responses using quadratic regression. The results showed that US significantly increased polyphenol content (up to 2200 mg FAGE/L) and antioxidant capacity (>100 μmol Trolox/g) under optimal conditions (60°C/30 min), although it reduced vitamin C by 32% compared to the control. Viscosity decreased in the treated samples to 3.1 mPa s, improving product fluidity, while the pH remained stable (3.6–3.7). Predictive models showed a high fit (R² >95%) for antioxidants and color. It is concluded that ultrasound improves bioactive extraction and technological properties at 52.4 °C and 31.2 min at 40 kHz. This technology offers a sustainable alternative for functional beverages, although it highlights the need for a balance between maximizing bioactive compounds and preserving thermolabile components. Future studies should evaluate the sensory impact and shelf life of products optimized using this technology.

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