This research explores the semi-solid fermentation (SSF) of quinoa (Chenopodium quinoa wild) in combination with mango–orange (Mangifera indica–Citrus sinensis) juice as a sustainable and innovative approach to food processing. Quinoa, renowned for its rich nutritional profile, presents challenges due to the presence of antinutrients that can inhibit nutrient absorption. By employing lactic acid bacteria (LAB) from kefir in the fermentation process, this study aims to enhance the bioavailability of essential nutrients while concurrently reducing the levels of antinutritional factors. The results indicate that fermentation leads to a significant increase in protein content, phytosterols, and antioxidant properties, while facilitating the conversion of bound phenolic compounds into more bioavailable forms. The incorporation of mango–orange juice enriched the nutritional profile of the product but lowered the pH, inhibiting microbial growth and necessitating a pH regulator to improve fermentation. Overall, this work contributes to the development of a probiotic-rich, functional beverage that not only supports food security but also aligns with sustainable food practices and promotes the nutritional health of populations where quinoa is a dietary staple. Further investigations will focus on optimizing fermentation conditions and exploring additional quinoa varieties to enhance product quality and health benefits.